Automated process for isolating and amplifying a target nucleic acid sequence

ABSTRACT

An automated analyzer for performing multiple diagnostic assays simultaneously includes multiple stations, or modules, in which discrete aspects of the assay are performed on fluid samples contained in reaction receptacles. The analyzer includes stations for automatically preparing a specimen sample, incubating the sample at prescribed temperatures for prescribed periods, preforming an analyte isolation procedure, and ascertaining the presence of a target analyte. An automated receptacle transporting system moves the reaction receptacles from one station to the next. The analyzer further includes devices for carrying a plurality of specimen tubes and disposable pipette tips in a machine-accessible manner, a device for agitating containers of target capture reagents comprising suspensions of solid support material and for presenting the containers for machine access thereto, and a device for holding containers of reagents in a temperature controlled environment and presenting the containers for machine access thereto. A method for performing an automated diagnostic assay includes an automated process for isolating and amplifying a target analyte. The process is performed by automatically moving each of a plurality of reaction receptacles containing a solid support material and a fluid sample between stations for incubating the contents of the reaction receptacle and for separating the target analyte bound to the solid support from the fluid sample. An amplification reagent is added to the separated analyte after the analyte separation step and before a final incubation step.

This application is a continuation of application Ser. No. 09/303,030,filed Apr. 30, 1999, now U.S. Pat. No. 6,335,166, which claims thebenefit of U.S. Provisional Application No. 60/083,927, filed May 1,1998.

1. FIELD OF THE INVENTION

The present invention relates to an automated analyzer for performingmultiple diagnostic assays simultaneously.

2. BACKGROUND OF THE INVENTION

None of the references described or referred to herein are admitted tobe prior art to the claimed invention.

Diagnostic assays are widely used in clinical diagnosis and healthscience research to detect or quantify the presence or amount ofbiological antigens, cell abnormalities, disease states, anddisease-associated pathogens, including parasites, fungi, bacteria andviruses present in a host organism or sample. Where a diagnostic assaypermits quantification, practitioners may be better able to calculatethe extent of infection or disease and to determine the state of adisease over time. In general, diagnostic assays are based either on thedetection of antigens (immunoassays) or nucleic acids (nucleicacid-based assays) belonging to an organism or virus of interest.

Nucleic acid-based assays generally include several steps leading to thedetection or quantification of one or more target nucleic acid sequencesin a sample which are specific to the organism or virus of interest. Thetargeted nucleic acid sequences can also be specific to an identifiablegroup of organisms or viruses, where the group is defined by at leastone shared sequence of nucleic acid that is common to all members of thegroup and is specific to that group in the sample being assayed. Thedetection of individual and groups of organisms and viruses usingnucleic acid-based methods is fully described by Kohne, U.S. Pat. No.4,851,330, and Hogan, U.S. Pat. No. 5,541,308.

The first step in a nucleic acid-based assay is designing a probe whichexhibits specificity, under stringent hybridization conditions, for anucleic acid sequence belonging to the organism or virus of interest.While nucleic acid-based assays can be designed to detect eitherdeoxyribonucleic acid (DNA) or ribonucleic acid (RNA), ribosomal RNA(rRNA), or the gene encoding rRNA (rDNA), is typically the preferrednucleic acid for detection of a prokaryotic or eukaryotic organism in asample. Ribosomal RNA target sequences are preferred because of theirrelative abundance in cells, and because rRNA contains regions ofsequence variability that can be exploited to design probes capable ofdistinguishing between even closely related organisms. (Ribosomal RNA isthe major structural component of the ribosome, which is the situs ofprotein synthesis in a cell.) Viruses, which do not contain rRNA, andcellular changes are often best detected by targeting DNA, RNA, or amessenger RNA (mRNA) sequence, which is a nucleic acid intermediate usedto synthesize a protein. When the focus of a nucleic acid-based assay isthe detection of a genetic abnormality, then the probes are usuallydesigned to detect identifiable changes in the genetic code, such as theabnormal Philadelphia chromosome associated with chronic myelocyticleukemia. See, e.g., Stephenson et al., U.S. Pat. No. 4,681,840.

When performing a nucleic acid-based assay, preparation of the sample isnecessary to release and stabilize target nucleic acids which may bepresent in the sample. Sample preparation can also serve to eliminatenuclease activity and remove or inactivate potential inhibitors ofnucleic acid amplification (discussed below) or detection of the targetnucleic acids. See, e.g., Ryder et al., U.S. Pat. No. 5,639,599, whichdiscloses methods for preparing nucleic acid for amplification,including the use of complexing agents able to complex with ferric ionscontributed by lysed red blood cells. The method of sample preparationcan vary and will depend in part on the nature of the sample beingprocessed (e.g., blood, urine, stool, pus or sputum). When targetnucleic acids are being extracted from a white blood cell populationpresent in a diluted or undiluted whole blood sample, a differentiallysis procedure is generally followed. See, e.g., Ryder et al., EuropeanPatent Application No. 93304542.9 and European Patent Publication No.0547267. Differential lysis procedures are well known in the art and aredesigned to specifically isolate nucleic acids from white blood cells,while limiting or eliminating the presence or activity of red blood cellproducts, such as heme, which can interfere with nucleic acidamplification or detection.

Before or after exposing the extracted nucleic acid to a probe, thetarget nucleic acid can be immobilized by target-capture means, eitherdirectly or indirectly, using a “capture probe” bound to a substrate,such as a magnetic bead. Examples of target-capture methodologies aredescribed by Ranki et al., U.S. Pat. No. 4,486,539, and Stabinsky, U.S.Pat. No. 4,751,177. Target capture probes are generally short sequencesof nucleic acid (i.e., oligonucleotide) capable of hybridizing, understringent hybridization conditions, with a sequence of nucleic acidwhich also contains the target sequence. Magnets in close proximity tothe reaction vessel are used to draw and hold the magnetic beads to theside of the vessel. Once the target nucleic acid is thus immobilized,the hybridized nucleic acid can be separated from non-hybridized nucleicacid by aspirating fluid from the reaction vessel and optionallyperforming one or more wash steps.

In most instances, it is desirable to amplify the target sequence usingany of several nucleic acid amplification procedures which are wellknown in the art. Specifically, nucleic acid amplification is theenzymatic synthesis of nucleic acid amplicons (copies) which contain asequence that is complementary to a nucleic acid sequence beingamplified. Examples of nucleic acid amplification procedures practicedin the art include the polymerase chain reaction (PCR), stranddisplacement amplification (SDA), ligase chain reaction (LCR), andtranscription-associated amplification (TAA). Nucleic acid amplificationis especially beneficial when the amount of target sequence present in asample is very low. By amplifying the target sequences and detecting theamplicon synthesized, the sensitivity of an assay can be vastlyimproved, since fewer target sequences are needed at the beginning ofthe assay to better ensure detection of nucleic acid in the samplebelonging to the organism or virus of interest.

Methods of nucleic acid amplification are thoroughly described in theliterature. PCR amplification, for instance, is described by Mullis etal. in U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,800,159, and in Methodsin Enzymology, 155:335-350 (1987). Examples of SDA can be found inWalker, PCR Methods and Applications, 3:25-30 (1993), Walker et al. inNucleic Acids Res., 20:1691-1996 (1992) and Proc. Natl. Acad. Sci.,89:392-396 (1991). LCR is described in U.S. Pat. Nos. 5,427,930 and5,686,272. And different TAA formats are provided in publications suchas Burg et al. in U.S. Pat. No. 5,437,990; Kacian et al. in U.S. Pat.Nos. 5,399,491 and 5,554,516; and Gingeras et al. in InternationalApplication No. PCT/US87/01966 and International Publication No. WO88/01302, and International Application No. PCT/US88/02108 andInternational Publication No. WO 88/10315.

Detection of a targeted nucleic acid sequence requires the use of aprobe having a nucleotide base sequence which is substantiallycomplementary to the targeted sequence or, alternatively, its amplicon.Under selective assay conditions, the probe will hybridize to thetargeted sequence or its amplicon in a manner permitting a practitionerto detect the presence of the targeted sequence in a sample. Effectiveprobes are designed to prevent non-specific hybridization with anynucleic acid sequence which will interfere with detecting the presenceof the targeted sequence. Probes may include a label capable ofdetection, where the label is, for example, a radiolabel, fluorescentdye, biotin, enzyme or chemiluminescent compound. Chemiluminescentcompounds include acridinium esters which can be used in a hybridizationprotection assay (HPA) and then detected with a luminometer. Examples ofchemiluminescent compounds and methods of labeling probes withchemiluminescent compounds can be found in Arnold et al., U.S. Pat. Nos.4,950,613, 5,185,439 and 5,585,481; and Campbell et al., U.S. Pat. No.4,946,958.

HPA is a detection method based on differential hydrolysis which permitsspecific detection of the acridinium ester-labeled probe hybridized tothe target sequence or amplicon thereof. HPA is described in detail byArnold et al. in U.S. Pat. Nos. 5,283,174 and 5,639,604. This detectionformat permits hybridized probe to be distinguished from non-hybridizedprobe in solution and includes both a hybridization step and a selectionstep. In the hybridization step, an excess of acridinium ester-labeledprobe is added to the reaction vessel and permitted to anneal to thetarget sequence or its amplicon. Following the hybridization step, labelassociated with unhybridized probe is rendered non-chemiluminescent inthe selection step by the addition of an alkaline reagent. The alkalinereagent specifically hydrolyzes only that acridinium ester labelassociated with unhybridized probe, leaving the acridinium ester of theprobe:target hybrid intact and detectable. Chemiluminescence from theacridinium ester of the hybridized probe can then be measured using aluminometer and signal is expressed in relative light units (RLU).

After the nucleic acid-based assay is run, and to avoid possiblecontamination of subsequent amplification reactions, the reactionmixture can be treated with a deactivating reagent which destroysnucleic acids and related amplification products in the reaction vessel.Such reagents can include oxidants, reductants and reactive chemicalswhich modify the primary chemical structure of a nucleic acid. Thesereagents operate by rendering nucleic acids inert towards anamplification reaction, whether the nucleic acid is RNA or DNA. Examplesof such chemical agents include solutions of sodium hypochlorite(bleach), solutions of potassium permanganate, formic acid, hydrazine,dimethyl sulfate and similar compounds. More details of a deactivationprotocol can be found in Dattagupta et al., U.S. Pat. No. 5,612,200.

When performed manually, the complexity and shear number of processingsteps associated with a nucleic acid-based assay introduce opportunitiesfor practitioner-error, exposure to pathogens, and cross-contaminationbetween assays. Following a manual format, the practitioner must safelyand conveniently juxtapose the test samples, reagents, waste containers,assay receptacles, pipette tips, aspirator device, dispenser device, andmagnetic rack for performing target-capture, while being especiallycareful not to confuse racks, test samples, assay receptacles, andassociated tips, or to knock over any tubes, tips, containers, orinstruments. In addition, the practitioner must carefully performaspirating and dispensing steps with hand-held, non-fixed instruments ina manner requiring precise execution to avoid undesirable contactbetween assay receptacles, aerosol formation, or aspiration of magneticparticles or other substrates used in a target-capture assay. As afurther precaution, the magnetic field in a manually performedtarget-capture assay is often applied to only one side of the assayreceptacle so that fluids can be aspirated through a pipette tipinserted along the opposite side of the assay receptacle. Althoughapplying a magnetic field to only one side of the assay receptacle is aless efficient means for performing a target capture assay, it isdesigned to prevent magnetic particles from being unnecessarilyaspirated as a result of practitioner inaccuracies.

A need exists for an automated diagnostic analyzer which addresses manyof the concerns associated with manual approaches to performing nucleicacid-based assays. In particular, significant advantages can be realizedby automating the various process steps of a nucleic acid-based assay,including greatly reducing the risk of user-error, pathogen exposure,contamination, and spillage, while significantly increasing through-putvolume. Automating the steps of a nucleic acid-based assay will alsoreduce the amount training required for practitioners and virtuallyeliminate sources of physical injury attributable to high-volume manualapplications.

SUMMARY OF THE INVENTION

The above-described needs are addressed by an automated clinicalanalyzer constructed and operated in accordance with aspects of thepresent invention. In general, the automated clinical analyzerintegrates and coordinates the operation of various automated stations,or modules, involved in performing one or more assays on a plurality ofreaction mixtures contained in reaction receptacles. The analyzer ispreferably a self-contained, stand alone unit. Assay specimen materialsand reaction receptacles, as well as the various solutions, reagents,and other materials used in performing the assays are preferably storedwithin the analyzer, as are the waste products generated when assays areperformed.

The analyzer includes a computer controller which runsanalyzer-controlling and assay-scheduling software to coordinateoperation of the stations of the analyzer and movement of each reactionreceptacle through the analyzer.

Reaction receptacles can be loaded in an input queue which sequentiallypresents each receptacle at a pick-up position to be retrieved by atransport mechanism, which automatically transports the reactionreceptacles between the stations of the analyzer.

Specimen containers are carried on a first ring assembly, and disposablepipette tips are carried on a second ring assembly. Containers of targetcapture reagent, including a suspension of solid support material, arecarried on an inner rotatable assembly constructed and arranged toselectively agitate the containers or present the containers for accessby the probe of an automatic robotic pipette system. Reaction mixtures,including fluid specimen material and target capture reagent, areprepared by the pipette system within each reaction receptacle.

The analyzer further includes receptacle mixers for mixing the contentsof a receptacle placed therein. The mixer may be in fluid communicationwith fluid containers and may include dispensers for dispensing one ormore fluids into the receptacle. One or more incubators carry multiplereceptacles in a temperature-controlled chamber and permit individualreceptacles to be automatically placed into and removed from thechamber. Magnetic separation wash stations automatically perform amagnetic separation wash procedure on the contents of a receptacleplaced in the station.

In the preferred method of operation, assay results may be ascertainedby the amount of light emitted from a receptacle at the conclusion ofthe appropriate preparation steps. Accordingly, the analyzer includes aluminometer for detecting and/or quantifying the amount of light emittedby the contents of the reaction receptacle. A deactivation queue may beprovided to deactivate the contents of a reaction receptacle placedtherein at the conclusion of the assay.

Reaction receptacles can be independently transported between stationsby the transport mechanism, and the stations can be operated in parallelto perform different assay procedures simultaneously on differentreaction receptacles, thereby facilitating efficient, high through-putoperation of the analyzer. Moreover, the present invention facilitatesarranging the various stations associated with a nucleic acid-basedassay onto a single, contained platform, thereby achieving efficientspace utilization.

Other objects, features, and characteristics of the present invention,including the methods of operation and the function and interrelation ofthe elements of structure, will become more apparent upon considerationof the following description and the appended claims, with reference tothe accompanying drawings, all of which form a part of this disclosure,wherein like reference numerals designate corresponding parts in thevarious figures.

DESCRIPTION OF THE DRAWINGS

FIG. 1 is a perspective view of an automated nucleic acid-baseddiagnostic analyzer according to the present invention;

FIG. 2 is a perspective view of the structural frame of the analyzer ofthe present invention;

FIG. 3 is a plan view of a portion of the assay processing deck of theanalyzer of the present invention;

FIG. 4 is an exploded perspective view of the assay processing deck;

FIG. 5 is a plan view of a specimen ring and a pipette tip wheel of theassay processing deck of the analyzer of the present invention;

FIG. 6 is a perspective view showing the specimen ring and the pipettetip wheel;

FIG. 6A is a partial cross-sectional view along the line 6A—6A in FIG.5;

FIG. 7 is a perspective view of a multi-axis mixer of the processingdeck of the analyzer of the present invention;

FIG. 8 is a plan view of the multi-axis mixer;

FIG. 9 is a side elevation of the multi-axis mixer;

FIG. 10 is a plan view of the multi-axis mixer with container holdersand a turntable cover removed therefrom;

FIG. 11 is a cross-sectional view of the multi-axis mixer taken in thedirection 11—11 in FIG. 10;

FIG. 12 is a perspective view of a drive assembly of the multi-axismixer;

FIG. 13 is a perspective view of a transport mechanism of the processingdeck of the analyzer of the present invention;

FIG. 14 is a perspective view of a manipulating hook mounting plate anda manipulating hook actuating mechanism of the transport mechanism, withthe manipulating hook member engaged with a reaction receptacle and in aretracted position;

FIG. 15 is the same as FIG. 14, except with the manipulating hook memberin the extended position;

FIG. 16 is an exploded perspective view of the transport mechanism;

FIG. 17 is a side-elevation of a temperature ramping station of theprocessing deck of the analyzer of the present invention;

FIG. 18 is a front-elevation of the temperature ramping station;

FIG. 19 is a perspective view of a rotary incubator of the processingdeck of the analyzer of the present invention;

FIG. 20 is an exploded view of a portion of a housing and access openingclosure mechanisms according to a first embodiment of the rotaryincubator;

FIG. 21 is a partial view of a skewed disk linear mixer of the rotaryincubator, shown engaged with a reaction receptacle employed in apreferred mode of operation of the analyzer of the present invention;

FIG. 22 is an exploded perspective view of the first embodiment of therotary incubator;

FIG. 23 is a perspective view of the rotary incubator according to asecond embodiment thereof;

FIG. 23A is an exploded perspective view of the second embodiment of therotary incubator;

FIG. 23B is a partial exploded perspective view of an access openingclosure mechanism of the second embodiment of the rotary incubator;

FIG. 23C is an exploded view of a receptacle carrier carousel of thesecond embodiment of the rotary incubator;

FIG. 24 is a perspective view of a magnetic separation wash station ofthe processing deck of the present invention with a side plate thereofremoved;

FIG. 25 is a partial transverse cross-section of the magnetic separationwash station;

FIG. 25A is a partial transverse cross-section of a tip of an aspiratingtube of the magnetic separation wash station with acontamination-limiting tiplet carried on the end thereof;

FIG. 26 is an exploded perspective view of a receptacle carrier unit, anorbital mixer assembly, and a divider plate of the magnetic separationwash station;

FIG. 27 is a partial cross-sectional view of a wash buffer dispensernozzle, an aspirator tube with a contamination-limiting tiplet engagedwith an end thereof, and a receptacle carrier unit of the magneticseparation wash station, showing a multi-tube unit reaction receptacleemployed in a preferred mode of operation of the analyzer carried in thereceptacle carrier unit and the aspirator tube andcontamination-limiting tiplet inserted into a receptacle vessel of themulti-tube unit;

FIG. 28 is a partial cross-sectional view of the wash buffer dispensernozzle, the aspirator tube, and the receptacle carrier unit of themagnetic separation wash station, showing the multi-tube unit carried inthe receptacle carrier unit and the aspirator tube engaging thecontamination-limiting tiplet held in a contamination-limiting elementholding structure of the multi-tube unit;

FIGS. 29A-29D show a partial cross-section of a first embodiment of atiplet stripping hole of a tiplet stripping plate of the magneticseparation wash station and a tiplet stripping operation using thetiplet stripping hole;

FIGS. 30A-30D show a partial cross-section of a second embodiment of atiplet stripping hole and a tiplet stripping operation using the tipletstripping hole;

FIG. 31A is a plan view of a third embodiment of a tiplet stripping holeof a tiplet stripping plate of the magnetic separation wash station;

FIGS. 31B-31C show a partial cross-section of the third embodiment ofthe tiplet stripping hole and a tiplet stripping operation using thetiplet;

FIG. 32 is a perspective view of an orbital mixer with a front platethereof removed;

FIG. 33 is an exploded view of the orbital mixer of the processing deckof the analyzer of the present invention;

FIG. 34 is a top-plan view of the orbital mixer;

FIG. 35 is a top perspective view of a reagent cooling bay of theprocessing deck of the analyzer of the present invention;

FIG. 36 is a top perspective view of a reagent cooling bay with thecontainer tray removed therefrom;

FIG. 37 is a bottom plan view of the reagent cooling bay;

FIG. 38 is an exploded view of the reagent cooling bay;

FIG. 39 is a top perspective view of a modular container tray of thereagent cooling bay;

FIG. 40 is a perspective view of a first embodiment of a luminometer ofthe processing deck of the analyzer of the present invention;

FIG. 41 is a partial exploded perspective view of the luminometer of thefirst embodiment;

FIG. 42A is a partial perspective view of a receptacle transportmechanism of the first embodiment of the luminometer;

FIG. 42B is an end view of the receptacle transport mechanism of thefirst embodiment of the luminometer;

FIG. 42C is a top view of the receptacle transport mechanism of thefirst embodiment of the luminometer;

FIG. 43 is a break away perspective view of a second embodiment of theluminometer of the present invention;

FIG. 44 is an exploded perspective view of a multi-tube unit doorassembly for the luminometer of the second embodiment;

FIG. 45 is an exploded perspective view of a shutter assembly for aphotosensor aperture for the luminometer of the second embodiment;

FIG. 45A is a perspective view of an aperture plate of the shutterassembly of the luminometer of the second embodiment;

FIG. 46 is a perspective view of a receptacle vessel positioner assemblyof the luminometer of the second embodiment, including a receptaclevessel positioner disposed within a receptacle vessel positioner frame;

FIG. 47 is a perspective view of the receptacle vessel positioner;

FIG. 48 is a side elevation of the receptacle vessel positionerassembly;

FIG. 49 is a perspective view showing the receptacle vessel positionerof the receptacle vessel positioner assembly operatively engaging amulti-tube unit employed in a preferred mode of operation of theanalyzer;

FIG. 50 is a perspective view of a multi-tube unit transport mechanismof the luminometer of the second embodiment;

FIG. 51 is a partial perspective view showing a multi-tube unittransport and drive screw of the multi-tube unit transport mechanism ofthe luminometer;

FIG. 52 is a perspective view of a lower chassis of the analyzer of thepresent invention;

FIG. 53 is a perspective view of a right-side drawer of the lowerchassis;

FIG. 54 is a perspective view of a left-side drawer of the lowerchassis;

FIG. 55 is a perspective view of a specimen tube tray employed in apreferred mode of operation of the analyzer of the present invention;

FIG. 56 is a top plan view of the specimen tube tray;

FIG. 57 is a partial cross-section of the specimen tube tray throughline “57—57” in FIG. 55;

FIG. 58 is a perspective view of a multi-tube unit employed in apreferred mode of operation of the analyzer of the present invention;

FIG. 59 is a side elevation of a contact-limiting pipette tipletemployed in a preferred mode of operation of the analyzer of the presentinvention and carried on the multi-tube unit shown in FIG. 58; and

FIG. 60 is an enlarged bottom view of a portion of the multi-tube unit,viewed in the direction of arrow “60” in FIG. 58.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

Analyzer Overview

An automated diagnostic analyzer according to the present invention isdesignated generally by reference number 50 in FIGS. 1 and 2. Analyzer50 includes a housing 60 built over an internal frame structure 62,preferably made of steel. The analyzer 50 is preferably supported oncaster wheels 64 structurally mounted to the frame structure 62 so as tomake the analyzer movable.

The various stations involved in performing an automated assay and theassay specimens are housed within housing 60. In addition, the varioussolutions, reagents, and other materials used in performing the assaysare preferably stored within the housing 60, as are the waste productsgenerated when assays are performed with the analyzer 50.

Housing 60 includes a test receptacle loading opening 68, which is shownin FIG. 1 to be disposed in a forwardly facing panel of the housing 60,but could as well be located in other panels of the housing 60. Apipette door 70 having a view window 72 and a carousel door 74 having aview window 76 are disposed above a generally horizontal work surface66. A forwardly protruding arcuate panel 78 accommodates a specimencarousel, which will be described below. A flip-up arcuate specimen door80 is pivotally attached to the housing so as to be vertically pivotalwith respect to arcuate panel 78 so as to provide access to a forwardportion of the specimen carousel behind the panel 78. Sensors indicatewhen the doors are closed, and the specimen door 80, the carousel door74, and the pipette door 70 are locked during analyzer operation. Thelocking mechanism for each door preferably consists of a hook attachedto a DC rotary solenoid (rated for continuous duty) with a springreturn. Preferred rotary solenoids are available from Lucas ControlSystems, of Vandalia, Ohio, model numbers L-2670-034 and L-1094-034.

An extension portion 102, preferably made of a transparent ortranslucent material, extends above the top portion of housing 60 so asto provide vertical clearance for moving components within the housing60.

The assays are performed primarily on a processing deck 200, which isthe general location of the various assay stations of the analyzer 50described below. For simplicity of the illustration, the processing deck200 is shown in FIG. 2 without any of the assay stations mountedthereon. The processing deck 200 comprises a datum plate 82 to which thevarious stations are directly or indirectly mounted. Datum plate 82preferably comprises a machined aluminum plate. The processing deck 200,also known as the chemistry deck, separates the interior of the housinginto the chemistry area, or upper chassis, above the datum plate 82 andthe storage areas, or lower chassis 1100, located below the datum plate82.

A number of fans and louvers are preferably provided in the upperchassis portion of the housing 60 to create air circulation throughoutthe upper chassis to avoid excessive temperatures in the upper chassis.

As the analyzer 50 of the present invention is computer controlled, theanalyzer 50 includes a computer controller, schematically represented asbox 1000 in FIG. 2, which runs high-level analyzer-controlling softwareknown as the “assay manager program”. The assay manager program includesa scheduler routine which monitors and controls test specimen movementthrough the chemistry deck 200.

The computer controller 1000 which controls the analyzer 50 may includea stand-alone computer system including a CPU, keyboard, monitor, andmay optionally include a printer device. A portable cart may also beprovided for storing and supporting the various computer components.Alternately, the computer hardware for running the analyzer-controllingsoftware may be integrally housed within the housing 60 of the analyzer50.

Low level analyzer control, such as control of electric motors andheaters used throughout the analyzer 50 and monitoring of fluid levelswithin bulk fluid and waste fluid containers, is performed by anembedded controller, preferably comprising a Motorola 68332microprocessor. Stepper motors used throughout the analyzer are alsopreferably controlled by preprogrammed, off-the-shelf, microprocessorchips available from E-M Technologies, Bala Cynwyd, Pa.

The processing deck 200 is shown schematically in FIGS. 3 and 4. FIG. 3represents a schematic plan view of a portion of the processing deck200, and FIG. 4 represents a schematic perspective view of theprocessing deck. The datum plate 82 forms the foundation of theprocessing deck 200 on which all stations are directly or indirectlyattached.

Processing deck 200 includes a reaction receptacle input queue 150 whichextends from opening 68 in front of housing 60. A plurality of reactionreceptacles are loaded in a stacked fashion in the input queue 150. Thepurpose of the input queue is to hold a prescribed number of reactionreceptacles and to sequentially present them at a pick-up position to beretrieved by a transport mechanism (described below). A reflectivesensor at the pick-up position verifies the presence of a receptacle atthat position. The input queue also includes a device for counting thenumber of receptacles resident therein at any given time.

A reaction receptacle shuttle assembly (not shown) within the queuemoves the receptacles along a receptacle advance path toward the pick-upposition. Optical sensors indicate when the shuttle assembly is in itshome and fully extended positions. The queue includes a drawer which maybe pulled out for loading the receptacles therein. Before the drawer isopened, however, it must be unlocked and the shuttle must disengage fromthe receptacle advance path. When the drawer is again closed, it islocked and the shuttle engages the receptacles and moves them toward thepick-up position. Optical sensors indicate when the drawer is closed andwhen the shuttle has engaged a receptacle. As each receptacle is removedfrom the pick-up position by the transport mechanism, the receptacleshuttle advances the receptacles one receptacle-width, so that the nextreceptacle is in the pick-up position.

The reaction receptacles are preferably integrally formed linear arraysof test tubes and known as multi-tube units, or MTUs. The preferredreaction receptacles (MTUs) will be described in more detail below.

A first ring assembly, which in the preferred embodiment comprises aspecimen ring 250, is mounted on a pivoting jig plate 130 at a distanceabove the datum plate 82. Specimen ring 250 is generally circular andpreferably holds up to nine specimen trays 300 in an annular fluidcontainer carrier portion thereof, and each of the specimen trayspreferably holds 20 specimen-containing containers, or test tubes 320.The specimen ring 250 is constructed and arranged to be rotatable abouta first generally vertical axis of rotation and delivers the specimentubes 320 to a specimen pipette assembly 450, preferably an automatedrobotic pipette system. The forward portion of specimen ring 250 isaccessible through the flip-up carousel door 80 provided in housing 60so that trays 300 of test tubes 320 can be easily loaded onto thespecimen ring 250 and unloaded from the specimen ring. Specimen ring 250is driven by a motor, as will be described in more detail below.

A second ring assembly, which in the preferred embodiment comprises apipette tip wheel 350, is located in an interior portion of the specimenring 250, so that at least a portion of the outer perimeter of thepipette tip wheel 350 is disposed radially inwardly of the innerperiphery of the ring 250. Pipette tip wheel 350 carries thereon aplurality of commercially available packages of pipette tips. Pipettetip wheel 350 is motor driven to rotate independently of specimen ring250 about a second axis of rotation that is generally parallel to thefirst axis of rotation of the specimen ring 250.

An inner rotatable assembly constructed and arranged to carry aplurality of fluid containers is provided at an interior portion of thepipette tip wheel 350. In the preferred embodiment, the inner rotatableassembly comprises a multi-axis mixer 400 located radially inside thepipette tip wheel 350 (i.e., the second ring assembly) and specimen ring250 (i.e., the first ring assembly). The multi-axis mixer 400 includes arotating turntable 414 that is rotatable about a third axis of rotationthat is generally parallel to the first and second axes of rotation andon which are mounted four independently and eccentrically rotatingcontainer holders 406. Each of the container holders 406 receives acontainer, preferably in the form of a plastic bottle, containing afluid suspension of magnetic particles with immobilized polynucleotidesand polynucleotide capture probes. Each container holder 406 isgenerally cylindrical in shape and includes an axis of symmetry, or axisof rotation. The multi-axis mixer 400 rotates each of the containerseccentrically with respect to the center of the holder 406, whilesimultaneously rotating the turntable 414 about its center so as toprovide substantially constant agitation of the containers to maintainthe magnetic particles in suspension within the fluid.

The specimen pipette assembly, or robot, 450 is mounted to the framestructure 62 (see FIG. 2) in a position above the specimen ring 250 andpipette tip wheel 350. The specimen pipette assembly 450 includes apipette unit 456 having a tubular probe 457 mounted on a gantry assemblyto provide X, Y, Z motion. Specifically, the pipette unit 456 islinearly movable in the Y-direction along a track 458 formed in alateral rail 454, and the lateral rail 454 is longitudinally movable inthe X-direction along a longitudinal track 452. The pipette unit 456provides vertical, or Z-axis motion of the probe 457. Drive mechanismswithin the specimen pipette assembly 450 position the pipette unit 456to the correct X, Y, Z coordinates within the analyzer 50 to pipettefluids, to wash the probe 457 of the pipette unit 456, to discard aprotective tip from an end of the probe 457 of the pipette unit 456, orto stow the pipette unit 456 during periods of nonuse, e.g., in a “home”position. Each axis of the specimen pipette assembly 450 is driven by astepper motor in a known and conventional manner.

The pipette assembly is preferably an off-the-shelf product. Presentlypreferred is the Robotic Sample Processor, model number RSP9000,available from Cavro Inc. of Sunnyvale, Calif. This model includes asingle gantry arm.

The specimen pipette assembly 450 is preferably coupled to a syringepump (not shown) (the Cavro XP 3000 has been used) and a DC drivendiaphragm system fluid wash pump (not shown). The syringe pump of thespecimen pipette assembly 450 is preferably mounted to the internalframe structure 62 within the housing 60 of the analyzer 50 at aposition above the left-hand side of the chemistry deck 200 and isconnected to pipette unit 456 by suitable tubing (not shown) or otherconduit structures.

A specimen preparation opening 252 is provided in the jig plate 130, sothat the specimen pipette assembly 450 can access a reaction receptacle160 in the input queue 150 located below the jig plate 130.

The specimen pipette assembly 450 of the analyzer 50 engages specimentubes 320 carried on the specimen ring 250 through openings 140, 142 ofan elevated cover plate 138 and engages pipette tips carried on thepipette tip wheel 350 near the back portions of the specimen ring 250and pipette tip wheel 350, respectively. Accordingly, an operator canhave access to the forward portions of specimen ring 250 and pipette tipwheel 350 through the carousel door opening 80 during operation of theanalyzer without interfering with pipetting procedures.

A tip wash/disposal station 340 is disposed adjacent to the specimenring 250 on the jig plate 130. Station 340 includes a tip disposal tube342 and a wash station basin 346. During specimen preparation, thepipette unit 456 of the specimen pipette assembly 450 can move intoposition above the wash station basin 346 where the tubular probe 457can be washed by pumping distilled water through the probe 457, thebasin of the wash station 346 being connected, preferably by a flexiblehose (not shown), to a liquid waste container in the lower chassis 1100.

The tip disposal tube 342 comprises an upstanding tubular member. Duringspecimen transfer from a specimen tube 320 to a reaction receptacle 160,an elongated pipette tip is frictionally secured onto the end of thetubular probe 457 of the pipette unit 456, so that specimen materialdoes not come into contact with the tubular probe 457 of the pipetteunit 456 when material is drawn from a specimen tube 320 and into theelongated pipette tip. After a specimen has been transferred from aspecimen tube 320, it is critical that the pipette tip used intransferring that specimen not be used again for another unrelatedspecimen. Therefore, after specimen transfer, the pipette unit 456 movesto a position above the tip disposal tube 342 and ejects the used,disposable pipette tip into the tip disposal tube 342 which is connectedto one of the solid waste containers carried in the lower chassis 1100.

An elongated pipette tip is preferably also frictionally secured to theprobe 457 for transferring target capture reagent from containerscarried on the multi-axis mixer 400 to a reaction receptacle 160.Following reagent transfer, the pipette tip is discarded.

As noted, the specimen ring 250, the pipette tip wheel 350, and themulti-axis mixer 400 are preferably mounted on a hinged jig plate 130(see FIGS. 5 and 6) supported above the datum plate 82. The jig plate130 is hinged at a back end 132 thereof (see FIG. 6) so that the plate,and the ring 250, the wheel 350, and the mixer 400 mounted thereon, canbe pivoted upwardly to permit access to the area of the chemistry deckbelow the jig plate.

A first, or right-side, transport mechanism 500 is mounted on the datumplate 82 below the jig plate 130 and specimen ring 250 on generally thesame plane as the input queue 150. Transport mechanism 500 includes arotating main body portion 504 defining a receptacle carrier assemblyand an extendible manipulating hook 506 mounted within the main body 504and extendible and retractable with respect thereto by means of apowered hook member drive assembly. Each of the reaction receptacles 160preferably includes manipulating structure that can be engaged by theextendible manipulating hook 506, so that the transport mechanism 500can engage and manipulate a reaction receptacle 160 and move it from onelocation on the processing deck 200 to another as the reactionreceptacle is sequentially moved from one station to another during theperformance of an assay within the reaction receptacle 160.

A second, or left-side, transport mechanism 502, of substantiallyidentical construction as first transport mechanism 500, is alsoincluded on the processing deck 200.

A plurality of receptacle parking stations 210 are also located belowthe jig plate 130. The parking stations 210, as their name implies, arestructures for holding specimen-containing reaction receptacles untilthe assay performing stations of the processing deck 200 of the analyzer50 are ready to accept the reaction receptacles. The reactionreceptacles are retrieved from and inserted into the parking stations210 as necessary by the transport mechanism 500.

A right-side orbital mixer 550 is attached to the datum plate 82 andreceives reaction receptacles 160 inserted therein by the right-sidetransport mechanism 500. The orbital mixer is provided to mix thecontents of the reaction receptacle 160. After mixing is complete, theright-side transport mechanism 500 removes the reaction receptacle fromthe right-side orbital mixer 550 and moves it to another location in theprocessing deck.

A number of incubators 600, 602, 604, 606, of substantially identicalconstruction are provided. Incubators 600, 602, 604, and 606 arepreferably rotary incubators. Although the particular assay to beperformed and the desired throughput will determine the desired numberof necessary incubators, four incubators are preferably provided in theanalyzer 50.

As will be described in more detail below, each incubator (600, 602,604, 606) has a first, and may also have a second, receptacle accessopening through which a transport mechanism 500 or 502 can insert areaction receptacle 160 into the incubator or retrieve a reactionreceptacle 160 from the incubator. Within each incubator (600, 602, 604,606) is a rotating receptacle carrier carousel which holds a pluralityof reaction receptacles 160 within individual receptacle stations whilethe receptacles are being incubated. For the nucleic acid-baseddiagnostic assay preferably performed on the analyzer 50 of the presentinvention, first rotary incubator 600 is a target capture and annealingincubator, second rotary incubator 602 is an active temperature andpre-read cool-down incubator (also known as an “AT incubator”), thirdrotary incubator 604 is an amplification incubator, and fourth rotaryincubator 606 is a hybridization protection assay incubator. Theconstruction, function, and role of the incubators in the overallperformance of the assay will be described in more detail below.

The processing deck 200 preferably also includes a plurality oftemperature ramping stations 700. Two such stations 700 are shownattached to the datum plate 82 between incubators 602 and 604 in FIG. 3.Additional ramping stations may be disposed at other locations on theprocessing deck 200 where they will be accessible by one of thetransport mechanisms 500, 502.

A reaction receptacle 160 may be placed into or removed from atemperature ramping station 700 by either transport mechanism 500 or502. Each ramping station 700 either raises or lowers the temperature ofthe reaction receptacle and its contents to a desired temperature beforethe receptacle is placed into an incubator or another temperaturesensitive station. By bringing the reaction receptacle and its contentsto a desired temperature before inserting it into one of the incubators(600, 602, 604, 606), temperature fluctuations within the incubator areminimized.

The processing deck 200 also includes magnetic separation wash stations800 for performing a magnetic separation wash procedure. Each magneticseparation wash station 800 can accommodate and perform a wash procedureon one reaction receptacle 160 at a time. Therefore, to achieve thedesired throughput, five magnetic separation wash stations 800 workingin parallel are preferred. Receptacles 160 are inserted into and removedfrom the magnetic separation wash stations 800 by the left-sidetransport mechanism 502.

A reagent cooling bay 900 is attached to the datum plate 82 roughlybetween the incubators 604 and 606. Reagent cooling bay 900 comprises acarousel structure having a plurality of container receptacles forholding bottles of temperature sensitive reagents. The carousel resideswithin a cooled housing structure having a lid with pipette-access holesformed therein.

A second, or left-side, orbital mixer 552, substantially identical toright-side orbital mixer 550, is disposed between incubators 606 and604. The left-side orbital mixer 552 includes dispenser nozzles andlines for dispensing fluids into the reaction receptacle resident withinthe left-side orbital mixer 552.

A reagent pipette assembly, or robot, 470 includes a double gantrystructure attached to the frame structure 62 (see FIG. 2) and isdisposed generally above the incubators 604 and 606 on the left-handside of the processing deck 200. Specifically, reagent pipette assembly470 includes pipette units 480 and 482. Pipette unit 480 includes atubular probe 481 and is mounted for linear movement, generally in theX-direction, along track 474 of lateral rail 476, and pipette unit 482,including a tubular probe 483, is also mounted for linear motion,generally in the X-direction, along track 484 of lateral rail 478.Lateral rails 476 and 478 can translate, generally in a Y-direction,along the longitudinal track 472. Each pipette unit 480, 482 providesindependent vertical, or Z-axis, motion of the respective probe 481,483. Drive mechanisms within the assembly 470 position the pipette units480, 482 to the correct X, Y, Z coordinates within the analyzer 50 topipette fluids, to wash the tubular probes 481, 483 of the respectivepipette units 480, 482, or to stow the pipette units 480, 482 duringperiods of nonuse, e.g., in “home” positions. Each axis of the pipetteassembly 470 is driven by a stepper motor.

The reagent pipette assembly 470 is preferably an off-the-shelf product.The presently preferred unit is the Cavro Robotic Sample Processor,model RSP9000, with two gantry arms.

The pipette units 480, 482 of the reagent pipette assembly 470 are eachpreferably coupled to a respective syringe pump (not shown) (the CavroXP 3000 has been used) and a DC driven diaphragm system fluid wash pump.The syringe pumps of the reagent pipette assembly 470 are preferablymounted to the internal frame structure 62 within the housing 60 of theanalyzer 50 at a position above the left-hand side of the chemistry deck200 and are connected to the respective pipette units 480, 482 bysuitable tubing (not shown) or other conduit structures.

Each pipette unit 480, 482 preferably includes capacitive level sensingcapability. Capacitive level sensing, which is generally known in themedical instrumentation arts, employs capacitance changes when thedielectric of a capacitor, formed by the pipette unit as one plate ofthe capacitor and the structure and hardware surrounding a containerengaged by the pipette unit as the opposite plate, changes from air tofluid to sense when the probe of the pipette unit has penetrated fluidwithin a container. By ascertaining the vertical position of the probeof the pipette unit, which may be known by monitoring the stepper motorwhich drives vertical movement of the pipette unit, the level of thefluid within the container engaged by the pipette unit may bedetermined.

Pipette unit 480 transfers reagents from the reagent cooling bay 900into reaction receptacles disposed within the incubator 606 or theorbital mixer 552, and pipette unit 482 transfers reagent materials fromthe reagent cooling bay 900 into reaction receptacles disposed withinthe amplification incubator 604 or the orbital mixer 552.

The pipette units 480, 482 use capacitive level sensing to ascertainfluid level within a container and submerge only a small portion of theend of the probe of the pipette unit to pipette fluid from thecontainer. Pipette units 480, 482 preferably descend as fluid ispipetted into the respective tubular probes 481, 483 to keep the end ofthe probes submerged to a constant depth. After drawing reagent into thetubular probe of the pipette unit 480 or 482, the pipette units create aminimum travel air gap of 10 μl in the end of the respective probe 481or 483 to ensure no drips from the end of the probe as the pipette unitis moved to another location above the chemistry deck 200.

The results of the assay preferably performed in the analyzer 50 of thepresent invention are ascertained by the amount of chemiluminescence, orlight, emitted from a receptacle vessel 162 at the conclusion of theappropriate preparation steps. Specifically, the results of the assayare determined from the amount of light emitted by label associated withhybridized polynucleotide probe at the conclusion of the assay.Accordingly, the processing deck 200 includes a luminometer 950 fordetecting and/or quantifying the amount of light emitted by the contentsof the reaction receptacle. Briefly, the luminometer 950 comprises ahousing through which a reaction receptacle travels under the influenceof a transport mechanism, a photomultiplier tube, and associatedelectronics. Various luminometer embodiments will be described in detailbelow.

The processing deck 200 also preferably includes a deactivation queue750. The assay performed in the analyzer 50 involves the isolation andamplification of nucleic acids belonging to at least one organism orcell of interest. Therefore, it is desirable to deactivate the contentsof the reaction receptacle 160, typically by dispensing a bleach-basedreagent into the reaction receptacle 160 at the conclusion of the assay.This deactivation occurs within the deactivation queue 750.

Following deactivation, the deactivated contents of the reactionreceptacle 160 are stored in one of the liquid waste containers of thelower chassis 1100 and the used reaction receptacle is discarded into adedicated solid waste container within the lower chassis 1100. Thereaction receptacle is preferably not reused.

Analyzer Operation

The operation of the analyzer 50, and the construction, cooperation, andinteraction of the stations, components, and modules described abovewill be explained by describing the operation of the analyzer 50 on asingle test specimen in the performance of one type of assay which maybe performed with analyzer 50. Other diagnostic assays, which requirethe use of one or more of the stations, components, and modulesdescribed herein, may also be performed with the analyzer 50. Thedescription herein of a particular assay procedure is merely for thepurpose of illustrating the operation and interaction of the variousstations, components, and modules of the analyzer 50 and is not intendedto be limiting. Those skilled in the art of diagnostic testing willappreciate that a variety of chemical and biological assays can beperformed in an automated fashion with the analyzer 50 of the presentinvention.

The analyzer 50 is initially configured for an assay run by loading bulkfluids into the bulk fluid storage bay of the lower chassis 1100 andconnecting the bulk fluid containers to the appropriate hoses (notshown).

The analyzer is preferably powered up in a sequential process, initiallypowering the stations, or modules, that will be needed early in theprocess, and subsequently powering the stations that will not be neededuntil later in the process. This serves to conserve energy and alsoavoids large power surges that would accompany full analyzer power-upand which could trip circuit breakers. The analyzer also employs a“sleep” mode during periods of nonuse. During sleep mode, a minimalamount of power is supplied to the analyzer, again to avoid large surgesnecessary to power-up an analyzer from complete shut-down.

A number of reaction receptacles 160, preferably in the form of plastic,integrally formed multiple-tube units (MTUs), which are described inmore detail below, are loaded through opening 68 into the input queue150. Henceforth, the reaction receptacles 160 will be referred to asMTUs, consistent with the preferred manner of using the analyzer 50.

The reaction receptacle shuttle assembly (not shown) within the inputqueue 150 moves the MTUs 160 from the loading opening 68 to the pick-upposition at the end of the queue 150. The right-side transport mechanism500 takes an MTU 160 from the end of the queue 150 and moves to a barcode reader (not shown) to read the unique bar code label on that MTUwhich identifies that MTU. From the bar code reader, the MTU is moved toan available specimen transfer station 255 below opening 252.

Multiple Tube Units

As shown in FIG. 58, an MTU 160 comprises a plurality of individualreceptacle vessels 162, preferably five. The receptacle vessels 162,preferably in the form of cylindrical tubes with open top ends andclosed bottom ends, are connected to one another by a connecting ribstructure 164 which defines a downwardly facing shoulder extendinglongitudinally along either side of the MTU 160.

The MTU 160 is preferably formed from injection molded polypropylene.The most preferred polypropylene is sold by Montell Polyolefins, ofWilmington, Del., product number PD701NW. The Montell material is usedbecause it is readily moldable, chemically compatible with the preferredmode of operation of the analyzer 50, and has a limited number of staticdischarge events which can interfere with accurate detection orquantification of chemiluminescence.

An arcuate shield structure 169 is provided at one end of the MTU 160.An MTU manipulating structure 166 to be engaged by one of the transportmechanisms 500, 502 extends from the shield structure 169. MTUmanipulating structure 166 comprises a laterally extending plate 168extending from shield structure 169 with a vertically extending piece167 on the opposite end of the plate 168. A gusset wall 165 extendsdownwardly from lateral plate 168 between shield structure 169 andvertical piece 167.

As shown in FIG. 60 the shield structure 169 and vertical piece 167 havemutually facing convex surfaces. The MTU 160 is engaged by the transportmechanisms 500, 502 and other components, as will be described below, bymoving an engaging member laterally (in the direction “A”) into thespace between the shield structure 169 and the vertical piece 167. Theconvex surfaces of the shield structure 169 and vertical piece 167provide for wider points of entry for an engaging member undergoing alateral relative motion into the space. The convex surfaces of thevertical piece 167 and shield structure 169 include raised portions 171,172, respectively, formed at central portions thereof. The purpose ofportions 171, 172 will be described below.

A label-receiving structure 174 having a flat label-receiving surface175 is provided on an end of the MTU 160 opposite the shield structure169 and MTU manipulating structure 166. Labels, such as scannable barcodes, can be placed on the surface 175 to provide identifying andinstructional information on the MTU 160.

The MTU 160 preferably includes tiplet holding structures 176 adjacentthe open mouth of each respective receptacle vessel 162. Each tipletholding structure 176 provides a cylindrical orifice within which isreceived a contact-limiting tiplet 170. The construction and function ofthe tiplet 170 will be described below. Each holding structure 176 isconstructed and arranged to frictionally receive a tiplet 170 in amanner that prevents the tiplet 170 from falling out of the holdingstructure 176 when the MTU 160 is inverted, but permits the tiplet 170to be removed from the holding structure 176 when engaged by a pipette.

As shown in FIG. 59, the tiplet 170 comprises a generally cylindricalstructure having a peripheral rim flange 177 and an upper collar 178 ofgenerally larger diameter than a lower portion 179 of the tiplet 170.The tiplet 170 is preferably formed from conductive polypropylene. Whenthe tiplet 170 is inserted into an orifice of a holding structure 176,the flange 177 contacts the top of structure 176 and the collar 178provides a snug but releasable interference fit between the tiplet 170and the holding structure 176.

An axially extending through-hole 180 passes through the tiplet. Hole180 includes an outwardly flared end 181 at the top of the tiplet 170which facilitates insertion of a pipette tubular probe (not shown) intothe tiplet 170. Two annular ridges 183 line the inner wall of hole 180.Ridges 183 provide an interference friction fit between the tiplet 170and a tubular probe inserted into the tiplet 170.

The bottom end of the tiplet 170 preferably includes a beveled portion182. When tiplet 170 is used on the end of an aspirator that is insertedto the bottom of a reaction receptacle, such as a receptacle vessel 162of an MTU 160, the beveled portion 182 prevents a vacuum from formingbetween the end of the tiplet 170 and the bottom of the reactionreceptacle vessel.

Lower Chassis

An embodiment of the lower chassis of the present invention is shown inFIGS. 52-54. The lower chassis 1100 includes a steel frame 1101 with ablack polyurethane powder coat, a pull-out drip tray 1102 disposed belowthe chassis, a right-side drawer 1104, and a left-side drawer 1106. Theleft-side drawer 1106 is actually centrally disposed within the lowerchassis 1100. The far left-side of the lower chassis 1100 houses variouspower supply system components and other analyzer mechanisms such as,for example, seven syringe pumps 1152 mounted on a mounting platform1154, a vacuum pump 1162 preferably mounted on the floor of the lowerchassis 1100 on vibration isolators (not shown), a power supply unit1156, a power filter 1158, and fans 1160.

A different syringe pump 1152 is designated for each of the fivemagnetic separation wash stations 800, one is designated for theleft-side orbital mixer 552, and one is designated for the deactivationqueue 750. Although syringe pumps are preferred, peristaltic pumps maybe used as an alternative.

The vacuum pump 1162 services each of the magnetic separation washstations 800 and the deactivation queue 750. The preferred rating of thevacuum pump is 5.3-6.5 cfm at 0″ Hg and 4.2-5.2 cfm at 5″ Hg. Apreferred vacuum pump is available from Thomas Industries, Inc. ofSheboygan, Wis., as model number 2750CGHI60. A capacitor 1172 is sold inconjunction with the pump 1162.

The power supply unit 1156 is preferably an ASTEC, model numberVS1-B5-B7-03, available from ASTEC America, Inc., of Carlsbad, Calif.Power supply unit 1156 accepts 220 volts ranging from 50-60 Hz, i.e.,power from a typical 220 volt wall outlet. Power filter 1158 ispreferably a Corcom model 20MV1 filter, available from Corcom, Inc. ofLibertyville, Ill. Fans 1160 are preferably Whisper XLDC fans availablefrom Comair Rotron, of San Ysidro, Calif. Each fan is powered by a 24VDCmotor and has a 75 cfm output. As shown in FIG. 52, the fans 1160 arepreferably disposed proximate a left-side outer wall of the lowerchassis 1100. The fans 1160 are preferably directed outwardly to drawair through the lower chassis from the right-side thereof to theleft-side thereof, and thus, to draw excess heat out of the lowerchassis.

Other power supply system components are housed in the back left-handside of the lower chassis 1100, including a power switch 1174,preferably an Eaton circuit breaker switch 2-pole, series JA/S,available from the Cutler-Hammer Division of Eaton Corporation ofCleveland, Ohio, and a power inlet module 1176 at which a power cord(not shown) for connecting the analyzer 50 to an external power sourceis connected. The power supply system of the analyzer 50 also includes aterminal block (not shown), for attaching thereto a plurality ofelectrical terminals, a solid state switch (not shown), which ispreferably a Crydom Series 1, model number D2425, available from CalSwitch, Carson City, Calif., for switching between different circuits,and an RS232 9-pin connector port for connecting the analyzer 50 to theexternal computer controller 1000.

The right-side drawer and left-side drawer bays are preferably closedbehind one or two doors (not shown) in front of the analyzer, whichis/are preferably locked by the assay manager program during operationof the analyzer. Microswitches are preferably provided to verifydoor-closed status. The far left bay is covered by a front panel. Endpanels are provided on opposite ends of the lower chassis to enclose thechassis.

Four leveler feet 1180 extend down from the four corners of the chassis1100. The leveler feet 1180 include threaded shafts with pads at thelower ends thereof. When the analyzer is in a desired location, the feet1180 can be lowered until the pads engage the floor to level andstabilize the analyzer. The feet can also be raised to permit theanalyzer to be moved on its casters.

Bulk fluids typically contained in the containers of the lower chassis1100 may include wash buffer (for washing immobilized target), distilledwater (for washing fixed pipette tips), diagnostic testing reagents,silicon oil (used as a floating fluid for layering over test reagentsand specimen), and a bleach-based reagent (used for sampledeactivation).

The right-side drawer 1104 is shown in detail in FIG. 53. The right-sidedrawer 1104 includes a box-like drawer structure with a front drawerhandle 1105. Although drawer handle 1105 is shown as a conventionalpull-type drawer handle, in the preferred embodiment of the analyzer 50,handle 1105 is a T-handle latch, such as those available from Southco,Inc. of Concordville, Pa. The drawer 1104 is mounted in the lowerchassis on slide brackets (not shown) so that the drawer 1104 can bepulled into and out of the lower chassis. A sensor (not shown) ispreferably provided for verifying that the drawer 1104 is closed. Thefront portion of the drawer includes bottle receptacles 1122 for holdingbottle 1128 (shown in FIG. 52), which is a dedicated pipette washwaste-containing bottle, and bottle 1130 (also shown in FIG. 52), whichis a dedicated waste bottle for containing waste from a magnetic wash,target-capture procedure. Bottle 1130 is preferably evacuated.

The analyzer 50 will not begin processing assays if any of the bottlesrequired in the lower chassis 1100 are missing. Bottle receptacles 1122preferably include bottle-present sensors (not shown) to verify thepresence of a bottle in each receptacle 1122. The bottle-present sensorsare preferably diffuse reflective type optical sensors available fromSUNX/Ramco Electric, Inc., of West Des Moines, Iowa, model EX-14A.

Right-side drawer 1104 further includes a waste bin 1108 for holdingtherein spent MTUs and specimen tips. Waste bin 1108 is an open boxstructure with a sensor mount 1112 at a top portion thereof for mountingthereon a sensor, preferably a 24VDC Opto-diffise reflector switch (notshown), for detecting whether the waste bin 1108 is full. Anotherdiffuse reflector type optical sensor (not shown) is positioned withinright-side drawer 1104 to verify that the waste bin 1108 is in place.Again, diffuse reflective type optical sensors available from SUNX/RamcoElectric, Inc., of West Des Moines, Iowa, model EX-14A, are preferred.

A deflector 1110 extends obliquely from a side of the waste bin 1108.Deflector 1110 is disposed directly below a chute through which spentMTUs are dropped into the waste bin 1108 and deflects the dropped MTUstoward the middle of the waste bin 1108 to avoid MTU pile-ups in acorner of the waste bin 1108. Deflector 1110 is preferably pivotallymounted so that it can pivot upwardly to a substantially verticalposition so that when a waste bag, which lines the waste bin 1108 andcovers the deflector 1110, is removed from the waste bin 1108, thedeflector 1110 will pivot upwardly with the bag as it is pulled out andtherefore will not rip the bag.

A printed circuit board (not shown) and cover 1114 can be mounted to thefront of the waste bin 1108. Sensor mounts 1116 and 1117 are alsomounted to the front of waste bin 1108. Sensors 1118 and 1119 aremounted on sensor mount 1116, and sensors 1120 and 1121 mounted onsensor mount 1117. Sensors 1118, 1119, 1120, and 1121 are preferably DCcapacitive proximity sensors. The upper sensors 1118, 1119 indicate whenthe bottles 1128 and 1130 are full, and the bottom sensors 1120, 1121indicate when the bottles are empty. Sensors 1118-1121 are preferablythose available from Stedham Electronics Corporation of Reno, Nev.,model number C2D45AN1-P, which were chosen because their relatively flatphysical profile requires less space within the tight confines of thelower chassis 1100 and because the Stedham sensors provide the desiredsensing distance range of 3-20 mm.

The analyzer 50 will preferably not begin performing any assays if theassay manager program detects that any of the waste fluid containers inthe right-side drawer 1104 are not initially empty.

The capacitive proximity sensors 1118-1121 and the bottle-present,waste-bin-present, and waste-bin-full optical sensors of the right-sidedrawer 1104 are connected to the printed circuit board (not shown)behind cover 1114, and the printed circuit board is connected to theembedded controller of the analyzer 50.

Because the right-side drawer 1104 cannot be pulled completely out ofthe lower chassis 1100, it is necessary to be able to pull the waste bin1108 forward so as to permit access to the waste bin for installing andremoving a waste bag liner. For this purpose, a handle 1126 is mountedto the front of the waste bin 1108 and teflon strips 1124 are disposedon the bottom floor of the right-side drawer 1104 to facilitate forwardand backward sliding of the waste bin 1108 in the drawer 1104 whenbottles 1128 and 1130 are removed.

Details of the left-side drawer 1106 are shown in FIG. 54. Left-sidedrawer 1106 includes a box-like structure with a front mounted handle1107 and is mounted within the lower chassis 1100 on slide brackets (notshown). Although handle 1107 is shown as a conventional pull-type drawerhandle, in the preferred embodiment of the analyzer 50, handle 1107 is aT-handle latch, such as those available from Southco, Inc. ofConcordville, Pa. A sensor is provided for verifying that the left-sidedrawer 1106 is closed.

Left-side drawer 1106 includes a tiplet waste bin 1134 with a mountingstructure 1135 for mounting thereon a tiplet-waste-bin-full sensor (notshown). A tiplet-waste-bin-present sensor is preferably provided in theleft-side drawer 1106 to verify that the tiplet waste bin 1134 isproperly installed. Diffuse reflective type optical sensors availablefrom SUNX/Ramco Electric, Inc., of West Des Moines, Iowa, model EX-14A,are preferred for both the tiplet-waste-bin-full sensor and thetiplet-waste-bin-present sensor.

Bundling structures 1132 are provided for securing and bundling varioustubing and/or wires (not shown) within the lower chassis 1100. Thebundling structures preferably used are Energy Chain Systemsmanufactured and sold by Igus, Inc. of East Providence, R.I.

A printed circuit board 1182 is mounted behind a panel 1184 which islocated behind the tiplet waste bin 1134. A solenoid valve mountingpanel 1186 is located below the tiplet waste bin 1134.

Left-side drawer 1106 includes a forward container-holding structure forholding therein six similarly sized bottles. The container structureincludes divider walls 1153, 1155, 1157, and 1159 and container blocks1151 having a curved bottle-conforming front edge, which together definesix container-holding areas. Lower sensors 1148 and upper sensors 1150(six of each) are mounted on the divider walls 1155, 1157, and 1159. Theupper and lower sensors 1148, 1150 are preferably DC capacitiveproximity sensors (preferably sensors available from Stedham ElectronicsCorporation of Reno, Nev., model number C2D45AN1-P, chosen for theirflat profile and sensing range). The upper sensors 1150 indicate whenthe bottles held in the container structure are full, and the lowersensors 1148 indicate when the bottles are empty. In the preferredarrangement, the left two bottles 1146 contain a detecting agent(“Detect I”), the middle two bottles 1168 contain silicon oil, and theright two bottles 1170 contain another detecting agent (“Detect II”).

Bottle-present sensors (not shown) are preferably provided in each ofthe container-holding areas defined by the container blocks 1151 and thedividing walls 1153, 1155, 1157, and 1159 to verify the presence ofbottles in each container-holding area. The bottle-present sensors arepreferably diffuse reflective type optical sensors available fromSUNX/Ramco Electric, Inc., of West Des Moines, Iowa, model EX-14A.

A large centrally located container receptacle 1164 holds a bottle 1140(shown in FIG. 52), preferably containing deionized water. Containerreceptacles 1166 (only one is visible in FIG. 54) hold bottles 1142 and1144 (also shown in FIG. 52) preferably containing a wash buffersolution. A dividing wall 1143 between the receptacle 1164 and 1166 hasmounted thereon sensors, such as sensor 1141, for monitoring the fluidlevel in the bottles 1140, 1142, and 1144. The sensors, such as sensor1141, are preferably DC capacitive proximity sensors (preferably sensorsavailable from Stedham Electronics Corporation of Reno, Nev., modelnumber C2D45AN1-P).

Container receptacles 1164 and 1166 preferably include bottle-presentsensors (not shown) for verifying that bottles are properly positionedin their respective receptacles. The bottle-present sensors arepreferably diffuse reflective type optical sensors available fromSUNX/Ramco Electric, Inc., of West Des Moines, Iowa, model EX-14A.

The analyzer 50 will not begin performing any assays if the assaymanager program determines that any of the bulk-fluid containers in theleft-side drawer 1106 are initially empty.

The capacitive proximity fluid level sensors, the various bottle-presentsensors, the tiplet-waste-bin-full sensor, and thetiplet-waste-bin-present sensors are all connected to the printedcircuit board 1182, and the printed circuit board 1182 is connected tothe embedded controller of the analyzer 50.

Four solenoid valves (not shown) are mounted below the solenoid valvemounting panel 1186. The solenoid valves connect bulk fluid bottleswhere fluids are stored in pairs of bottles, i.e., the bottles 1140,1142 containing wash buffer solution, the two bottles 1146 containingthe “Detect I” agent, the two bottles 1168 containing oil, and the twobottles 1170 containing the “Detect II” agent. The solenoid valves, inresponse to signals from the respective capacitive proximity sensors,switch bottles from which fluid is being drawing when one of the twobottles containing the same fluid is empty. In addition, the solenoidvalves may switch bottles after a prescribed number of tests areperformed. The preferred solenoid valves are teflon solenoid valvesavailable from Beco Manufacturing Co., Inc. of Laguna Hills, Calif.,model numbers S313W2DFRT and M223W2DFRLT. The two different modelnumbers correspond to solenoid valves adapted for use with two differenttube sizes. Teflon solenoid valves are preferred because they are lesslikely to contaminate fluids flowing through the valves and the valvesare not damaged by corrosive fluids flowing through them.

Bottle 1136 (see FIG. 52) is a vacuum trap held in a vacuum trap bracket1137, and bottle 1138 contains a deactivating agent, such asbleach-containing reagent. Again, bottle-present sensors are preferablyprovided to verify the presence of bottles 1136 and 1138.

A hand-held bar code scanner 1190 may be provided in the lower chassis1100 for scanning information provided on scannable container labelsinto the assay manager program. Scanner 1190 is connected by a cord toprinted circuit board 1182 of the left-side drawer 1106 and ispreferably stowed on a bracket (not show) mounted on dividing wall 1143.Scanners available from Symbol Technologies, Inc., of Holtsville, N.Y.,series LS2100, are preferred.

Specimen Ring and Specimen Tube Trays

Specimens are contained in the specimen tubes 320, and the tubes 320 areloaded into the tube trays 300 outside the analyzer 50. The trays 300carrying the specimen tubes 320 are placed onto the specimen ring 250through the access opening provided by opening the flip-up carousel door80.

Referring to FIGS. 5 and 6, the first ring assembly, or specimen ring,250 is formed of milled, unhardened aluminum and includes a raised ringstructure defining an annular trough 251 about the outer periphery ofring 250 with a plurality of raised, radially extending dividers 254extending through trough 251. Preferably, nine dividers 254 divide thetrough 251 into nine arcuate specimen tube tray-receiving wells 256. Thetrough 251 and wells 256 define an annular fluid container carrierportion constructed and arranged to carry a plurality of containers aswill be described below.

Specimen ring 250 is preferably rotationally supported by three120°-spaced V-groove rollers 257, 258, 260 which engage a continuousV-ridge 262 formed on the inner periphery of ring 250, as shown in FIGS.5, 6, and 6A so that the ring 250 is rotatable about a first centralaxis of rotation. The rollers are preferably made by Bishop-WisecarverCorp. of Pittsburg, Calif., model number WLSSX. Rollers 257 and 260 arerotationally mounted on fixed shafts, and roller 258 is mounted on abracket which pivots about a vertical axis and is spring biased so as tourge roller 258 radially outward against the inner periphery of ring250. Having two fixed rollers and one radially movable roller allows thethree rollers to accommodate an out-of-round inner periphery of the ring250.

Specimen ring 250 is driven by stepper motor 264 (VEXTA stepper motorsavailable from Oriental Motor Co., Ltd. of Tokyo, Japan as model numberPK266-01A are preferred) via continuous belt 270 (preferably availablefrom SDP/SI of New Hyde Park, N.Y., as model number A6R3M444080) whichextends over guide rollers 266, 268 and around the outer periphery ofring 250. A home sensor and a sector sensor (not shown), preferablyslotted optical sensors, are provided adjacent the ring 250 at arotational home position and at a position corresponding to one of thespecimen tube tray receiving wells 256. The ring 250 includes a homeflag (not shown) located at a home position on the wheel and nineequally-spaced sector flags (not shown) corresponding to the positionsof each of the nine specimen tube tray receiving wells 256. The homeflag and sector flags cooperate with the home sensor and sector sensorsto provide ring position information to the assay manager program and tocontrol the ring 250 to stop at nine discrete positions corresponding toestablished coordinates for user re-load and access by pipette unit 450.Preferred sensors for the home sensor and sector sensor are Optekslotted optical sensors, model number OPB857, available from Optek ofCarrollton, Tex.

A specimen cover is disposed over a portion of the annular fluidcontainer carrier portion, or trough 251, and comprises an arcuate coverplate 138 fixed in an elevated position with respect to the wheel 250 onthree mounting posts 136. Plate 138 has an arcuate shape generallyconforming to the curve of the trough 251. A first opening 142 is formedin the plate 138, and a second opening 140 is formed in the plate 138 ata greater radial distance from the axis of rotation of ring 250 thanopening 142 and at a circumferentially-spaced position from opening 142.

Referring to FIGS. 55-57, each specimen tube tray 300 comprises a testtube rack structure that is curved to conform to the curvature of thering 250. Each tray 300 comprises a central wall structure 304 withlateral end walls 303 and 305 disposed on either end of wall 304. Afloor 312 extends across the bottom of the tray 300. The principlepurposes of specimen tube 11 tray 300 are to hold specimen tubes on thespecimen ring 250 for access by the specimen pipette assembly 450 and tofacilitate loading and unloading of multiple specimen tubes into andfrom the analyzer.

A plurality of Y-shaped dividers 302 are equidistantly spaced alongopposite edges of the tray 300. Each two adjacent dividers 302 define atest-tube receiving area 330. End wall 303 includes inwardly bentflanges 316 and 318, and end wall 305 includes inwardly bent flanges 326and 328. The respective inwardly bent flanges of end walls 303 and 305along with the end-most of the dividers 302 define the end-most tubereceiving areas 332. The receiving areas 330, 332 are arcuately alignedalong two arcuate rows on opposite sides of central wall structure 304

Referring to FIG. 57, within each tube receiving area 330, 332, a leafspring element 310 is attached to central wall 304. Leaf spring element310, preferably formed of stainless spring steel, elastically deflectswhen a test tube 320 is inserted into the tube-receiving area 330 or 332and urges the tube 320 outwardly against the dividers 302. Thus, thetube 320 is secured in an upright orientation. The shape of the dividers302 and the elasticity of the leaf spring elements 310 allow the tray300 to accommodate specimen tubes of various shapes and sizes, such astubes 320 and 324. Each tray 300 preferably includes nine dividers 302along each edge to form, along with end walls 303 and 305, tentube-receiving areas 330, 332 on each side of central wall structure 304for a total of twenty tube-receiving areas per tray. Indicia fordesignating tube-receiving areas 330 and 332, such as raised numerals306, may be provided on the tray, such as on central wall 304.

Each tray 300 may also include boss structures 308, shown in theillustrated embodiment to be integrally formed with the end-mostdividers 302. An upright inverted U-shaped handle (not shown) may beattached to the tray at boss structures 308 or some other suitablelocation. Upright handles can facilitate handling of the tray 300 whenloading and unloading the tray 300 through the arcuate carousel door 80,but are not necessarily preferred.

A gap is provided between adjacent dividers 302 so that bar-code labels334, or other readable or scannable information, on the tubes 320 isaccessible when the tube is placed in the tray 300. When a tray 300carried on wheel 250 passes beneath the plate 138 of the specimen cover,one tube 320 in a curved row at a radially-inward position with respectto wall structure 304 will be aligned with first opening 142 and anothertube 320 in a curved row at a radially-outward position with respect towall 304 will be aligned with second opening 140. The ring 250 isindexed to sequentially move each tube 320 beneath the openings 140, 142to permit access to the tubes.

Referring again to FIG. 5, bar code scanners 272 and 274 are disposedadjacent the ring 250. Opticon, Inc. scanners, model numberLHA2126RR1S-032, available from Opticon, Inc. of Orangeburg, N.Y., arepreferred. Scanner 272 is located outside ring 250, and scanner 274 isdisposed inside ring 250. Scanners 272 and 274 are positioned to scanbar code data labels on each specimen tube 320 carried in the specimentube tray 300 as the ring 250 rotates a tray 300 of specimen tubes 320past the scanners 272, 274. In addition, the scanners 272, 274 scan thebar code label 337 (see FIG. 55) on the outer portion of bent flanges316 and 318 of end wall 303 of each tray 300 as the tray 300 is broughtinto the specimen preparation area. Various information, such asspecimen and assay identification, can be placed on the tubes and/oreach tray 300, and this information can be scanned by the scanners 272,274 and stored in the central processing computer. If no specimen tubeis present, the tray 300 presents a special code 335 (see FIG. 55) to beread by the scanners 272, 274.

Pipette Tip Wheel

As shown primarily in FIGS. 5 and 6, a second ring assembly of thepreferred embodiment is a pipette tip wheel 350 and comprises a circularring 352 at a bottom portion thereof, a top panel 374 defining acircular inner periphery and five circumferentially-spaced,radially-protruding sections 370, and a plurality of generallyrectangular risers 354 separating the top panel 374 from the ring 352and preferably held in place by mechanical fasteners 356 extendingthrough the top panel 374 and ring 352 into the risers 354. Fiverectangular openings 358 are formed in the top panel 374 proximate eachof the sections 370, and a rectangular box 376 is disposed beneath panel374, one at each opening 358. Top panel 374, ring 352, and risers 354are preferably made from machined aluminum, and boxes 376 are preferablyformed from stainless steel sheet stock.

The openings 358 and associated boxes 376 are constructed and arrangedto receive trays 372 holding a plurality of disposable pipette tips. Thepipette tip trays 372 are preferably those manufactured and sold byTECAN (TECAN U.S. Inc., Research Triangle Park, N.C.) under the tradename “Disposable Tips for GENESIS Series”. Each tip has a 1000 μlcapacity and is conductive. Each tray holds ninety-six elongateddisposable tips.

Lateral slots 378 and longitudinal slots 380 are formed in the top panel374 along the lateral and longitudinal edges, respectively, of eachopening 358. The slots 378, 380 receive downwardly-extending flanges(not shown) disposed along the lateral and longitudinal edges of thetrays 372. The slots 378, 380 and associated flanges of the trays 372serve to properly register the trays 372 with respect to openings 358and to hold the trays 372 in place on the panel 374.

Pipette tip wheel 350 is preferably rotationally supported by three120°-spaced V-groove rollers 357, 360, 361 which engage a continuousV-ridge 362 formed on the inner periphery of ring 352, as shown in FIGS.5, 6, and 6A, so that the pipette tip wheel 350 is rotatable about asecond central axis of rotation that is generally parallel to the firstaxis of rotation of the specimen ring 250. The rollers are preferablymade by Bishop-Wisecarver Corp. of Pittsburg, Calif., model numberW1SSX. Rollers 357 and 360 are rotationally mounted on fixed shafts, androller 361 is mounted on a bracket which pivots about a vertical axisand is spring biased so as to urge roller 361 radially outwardly againstthe inner periphery of ring 352. Having two fixed rollers and oneradially movable roller allows the three rollers to accommodate anout-of-round inner periphery of ring 352. In addition, the wheel 350 canbe easily installed and removed by merely pushing pivoting roller 361radially inwardly to allow the ring 352 to move laterally to disengagecontinuous V-ridge 362 from the fixed V-groove rollers 357, 360.

Pipette tip wheel 350 is driven by a motor 364 having a shaft-mountedspur gear which meshes with mating gear teeth formed on an outerperimeter of ring 352. Motor 364 is preferably a VEXTA gear head steppermotor, model number PK243-A1-SG7.2, having a 7.2:1 gear reduction andavailable from Oriental Motor Co., Ltd. of Tokyo, Japan. A gear headstepper motor with a 7.2:1 gear reduction is preferred because itprovides smooth motion of the pipette tip wheel 350, where the spur gearof the motor 364 is directly engaged with the ring 352.

A home sensor and a sector sensor (not shown), preferably slottedoptical sensors, are provided adjacent the pipette tip wheel 350 at arotational home position and at a position of one of the boxes 376. Thepipette tip wheel 350 includes a home flag (not shown) located at a homeposition on the wheel and five equally-spaced sector flags (not shown)corresponding to the positions of each of the five boxes 376. The homeflag and sector flags cooperate with the home sensor and sector sensorsto provide wheel position information to the assay manager program andto control the pipette tip wheel 350 to stop at five discrete positionscorresponding to established coordinates for user re-load and access bypipette unit 450. Preferred sensors for the home sensor and sectorsensor are Optek Technology, Inc. slotted optical sensors, model numberOPB980, available from Optek Technology, Inc. of Carrollton, Tex.

Multi-Axis Mixer

Referring to FIGS. 7-12, the multi-axis mixer 400 includes a rotatingturntable structure 414 (see FIG. 10) rotatably mounted on a centershaft 428 supported in center bearings 430 to a fixed base 402 mountedto the jig plate 130 by means of mechanical fasteners (not shown)extending through apertures 419 formed about the outer periphery of thefixed base 402. A cover member 404 is attached to and rotates withturntable 414.

Turntable 414 is preferably in the form of a right angle crosscomprising three 90°-spaced rectangular arms 444 of equal lengthextending radially outwardly from the center of the turntable 414 and afourth arm 445 having an extension 417 making arm 445 slightly longerthan arms 444. As shown in FIGS. 10-12, the center portion of turntable414 is connected to center shaft 428 by a screw 429.

Four container holders 406 are disposed on the ends of the arms 444 and445 of turntable frame 414. Each container holder 406 is attached to oneof four vertical shafts 423, which are rotatably supported in containerholder bearings 415. Container holder bearings 415 are pressed into thearms 444, 445 of the turntable 414 and are disposed at equal radialdistances from shaft 428.

The cover member 404 includes four circular openings withupwardly-turned peripheral flanges 401 through which shafts 423 extend.Upward flanges 401 can advantageously prevent spilled liquids fromflowing into the openings.

The container holders 406 comprise generally cylindrical members havingan open bottom and an open top for receiving and holding a container440, preferably a plastic bottle, of target capture reagent.

The target capture reagent used with the preferred assay includesmagnetically responsive particles with immobilized polynucleotides,polynucleotide capture probes, and reagents sufficient to lyse cellscontaining the targeted nucleic acids. After cell lysis, targetednucleic acids are available for hybridization under a first set ofpredetermined hybridization conditions with one or more capture probes,with each capture probe having a nucleotide base sequence region whichis capable of hybridizing to a nucleotide base sequence region containedon at least one of the targeted nucleic acids. Under a second set ofpredetermined hybridization conditions, a homopolymer tail (e.g.,oligo(dT)) of the immobilized polynucleotides is capable of hybridizingwith a complementary homopolymer tail (e.g., oligo(dA)) contained on thecapture probe, thereby immobilizing targeted nucleic acids.Target-capture methods and lysing procedures are well known in the artand are described more fully in the background section supra.

A container retainer spring 408 spans a lateral slot formed in the wallof each container holder 406 and helps to hold the container 440 withinthe container holder 406 by urging the container 440 toward a portion ofthe inner peripheral wall of the holder 406 opposite the spring 408.

Each container holder 406 is secured to an associated vertical shaft 423by a shaft block structure 432. Shaft block structure 432 includescurved end portions which conform to the inside of the cylindricalcontainer holder 406, and the container holder 406 is secured to theblock 432 by fasteners 434. A generally circular aperture 449 receivesthe shaft 423. A slot 438 extends from aperture 449 to an end of theblock 432 which does not extend all the way to the inside of thecontainer holder 406, and a second slot 436 extends from an edge of theblock 432 generally perpendicularly to slot 438 so as to define acantilevered arm 435. A machine screw 437 extends through a through-hole441 formed laterally through block 432 and into a threaded hole 447formed laterally through arm 435. As screw 437 is tightened, arm 435deflects, thus tightening aperture 449 around shaft 423.

The shaft block structure 432, the shaft 423, and the container holderbearings 415 associated with each container holder 406 define apreferred container holder mounting structure associated with eachcontainer holder 406 that is constructed and arranged to mount thecontainer holder 406 to the turntable 414 and permit the containerholder 406 to rotate about an axis of rotation 412 of the shaft 423.

Container holder planetary gears 422 are attached to the opposite endsof shafts 423. The planetary gears 422 operatively engage a stationarysun gear 416. A drive pulley 418 is attached to center shaft 428 and iscoupled to a drive motor 420 by a drive belt (not shown). Drive motor420 is preferably mounted so as to extend through an opening (not shown)in the jig plate 130 below the base 402. Drive motor 420 is preferably astepper motor, and most preferably a VEXTA stepper motor, model numberPK264-01A, available from Oriental Motor Co., Ltd. of Tokyo, Japan. Thedrive motor 420, via the drive belt and drive pulley 418, rotates thecenter shaft 428 and the turntable 414 attached thereto. As theturntable frame 414 rotates about the center line of center shaft 428,the planetary gears 422 engaged with sun gear 416 cause the shafts 423and container holders 406 attached thereto to rotate at the ends of thearms 444 of the turntable frame 414. Each container holder 406 ispreferably mounted such that the axis of rotation 410 thereof is offsetfrom the axis of rotation 412 of the associated shaft 423. Thus, eachcontainer holder 406 rotates eccentrically about axis 412 of theassociated shaft 423. Accordingly, the planetary gears 422 and the sungear 416 constitute rotational motion coupling elements constructed andarranged to cause the container holders 406 to rotate about therespective axes of rotation of the shafts 423 as the turntable 414rotates about the axis of rotation of the shaft 428.

A bar code scanner device 405 is preferably mounted on a bracket 403 andreads bar code information of the containers 440 through a scanner slot407 formed in each container holder 406. The preferred scanner is amodel number NFT1125/002RL scanner, available from Opticon, Inc. ofOrangeburg, N.Y.

The multi-axis mixer 400 usually rotates during operation of theanalyzer 50 to agitate the fluid contents of the containers 440 tothereby keep the target capture reagent in suspension, stopping onlybriefly to permit pipette unit 456 to withdraw an amount of mixture fromone of the containers. Pipette unit 456 draws mixture from a bottle atthe same location each time. Therefore, it is desirable to monitor thepositions of the bottles so that the bottle from which mixture iswithdrawn each time can be specified.

Four optical slotted sensors 426, each comprising an optical emitter anddetector, are stationed around the periphery of fixed base 402, spacedat 90° intervals. Optical sensors available from Optek Technology, Inc.of Carrollton, Tex., model number OPB490P11, are preferred. A sensor tab424 extends down from extension 417 at the end of arm 445 of theturntable 414. When sensor tab 424 passes through a sensor 426, thecommunication between the emitter and detector is broken thus giving a“container present” signal. The tab 424 is only provided at onelocation, e.g., the first container location. By knowing the position ofthe first container, the positions of the remaining containers, whichare fixed relative to the first container, are also known.

Power and control signals are provided to the multi-axis mixer 400 via apower and data connector. While the multi-axis mixer 400 provides mixingby rotation and eccentric revolution, other mixing techniques, such asvibration, inversion, etc. may be used.

Specimen Preparation Procedure

To begin specimen preparation, the pipette unit 456 moves to transfertarget capture reagent, preferably mag-oligo reagent, from a container440 carried on the multi-axis mixer 400 into each of the receptaclevessels 162 of the MTU 160. The target capture reagent includes asupport material able to bind to and immobilize a target analyte. Thesupport material preferably comprises magnetically responsive particles.At the beginning of the specimen preparation procedure, the pipette unit456 of the right-side pipette assembly 450 moves laterally andlongitudinally to a position in which the probe 457 is operativelypositioned over a pipette tip in one of the trays 372.

The tip trays 372 are carried on the pipette tip wheel 350 so as to beprecisely positioned to achieve proper registration between the pipettetips and the tubular probe 457 of the pipette unit 456. The pipette unit456 moves down to insert the free end of the tubular probe 457 into theopen end of a pipette tip and frictionally engage the pipette tip. TheCavro processors preferably used for pipette unit 456 includes a collar(not shown), which is unique to Cavro processors. This collar is movedslightly upwardly when a pipette tip is frictionally engaged onto theend of the tubular probe 457, and the displaced collar trips anelectrical switch on the pipette unit 456 to verify that a pipette tipis present. If tip pick-up is not successful (e.g., due to missing tipsin the trays 372 or a misalignment), a missing tip signal is generatedand the pipette unit 456 can move to re-try tip engagement at adifferent tip location.

The assay manager program causes the multi-axis mixer 400 to brieflystop rotating so that the pipette unit 456 can be moved to a positionwith the tubular probe 457 and attached pipette tip of the pipette unit456 aligned over one of the stationary containers 440. The pipette unit456 lowers the pipette tip attached to the tubular probe 457 into thecontainer 440 and draws a desired amount of target capture reagent intothe pipette tip. The pipette unit 456 then moves the probe 457 out ofthe container 440, the multi-axis mixer 400 resumes rotating, and thepipette unit 456 moves to a position above opening 252 and the specimentransfer station 255. Next, the pipette unit 456 descends, moving thepipette tip and the tubular probe 457 through the opening 252, anddispenses a required amount of target capture (typically 100-500 μl)into one or more of the receptacle vessels 162 of the MTU 160. It ispreferred that the target capture reagent is drawn only into the pipettetip and not into the probe 457 itself. Furthermore, it is preferred thatthe pipette tip be of sufficient volumetric capacity to hold enoughreagent for all five vessels 162 of the MTU 160.

After target capture reagent transfer, the pipette unit 456 then movesto a “tip discard” position above tip disposal tube 342, where thedisposable pipette tip is pushed or ejected off of the end of thetubular probe 457 of the pipette unit 456, and falls through tube 342toward a solid waste container. An optical sensor (not shown) isdisposed adjacent to tube 342, and before tip discard, the specimenpipette assembly 450 moves the pipette unit 456 into a sensing positionof the sensor. The sensor detects whether a tip is engaged with the endof the tubular probe 457 to verify that the tip is still held on thetubular probe 457 of the pipette unit 456, thereby confirming that thetip was on the tubular probe 457 throughout specimen preparation. Apreferred sensor is a wide-gap slotted optic sensor, model OPB900W,available from Optek Technology, Inc. of Carrollton, Tex.

Preferably, the pipette tip is ejected by the collar (not shown) on thetubular probe 457 of pipette unit 456. The collar engages a hard stopwhen the tubular probe 457 is raised, so that as the probe 457 continuesto ascend, the collar remains fixed and engages an upper end of thepipette tip, thereby forcing it off the tubular probe 457.

After pipetting the target capture and discarding the pipette tip, theprobe 457 of the pipette unit 456 can be washed by running distilledwater through the tubular probe 457 at the tip wash station basin 346.The tip wash water is collected and drains down into a liquid wastecontainer.

Following the reagent dispensing procedure, the pipette unit 456 on theright pipette assembly 450 moves laterally and longitudinally to aposition in which the tubular probe 457 of the pipette unit 456 iscentered over a new pipette tip on one of the tip trays 372. Aftersuccessful tip engagement, the pipette unit 456 moves back over thespecimen ring 250, adjacent to the specimen preparation opening 252 andwithdraws a test specimen (about 25-900 μl) from a specimen tube 320that is aligned with one of the openings 140, 142 of the cover plate138. Note that both openings 140, 142 include upwardly extendingperipheral flanges to prevent any fluids spilled onto the plate 138 fromrunning into the openings 140, 142. The pipette unit 456 then moves overthe MTU 160 in the specimen transfer station 255, moves down throughopening 252, and dispenses test specimen into one of the receptaclevessels 162 of the MTU 160 containing target capture reagent. Pipetteunit 456 then moves to the “tip discard” position above the tip disposaltube 342, and the disposable pipette tip is ejected into the tube 342.Pipette unit 456 then picks up a new disposable pipette tip from thepipette tip wheel 350, the specimen ring 250 indexes so that a newspecimen tube is accessible by the pipette unit 456, unit 456 moves toand draws specimen fluid from the specimen tube into the disposablepipette tip, the pipette unit 456 then moves to a position above thespecimen transfer station 255, and dispenses specimen fluid into adifferent receptacle vessel 162 containing target capture reagent. Thisprocess is preferably repeated until all five receptacle vessels 162contain a combination of fluid specimen sample and target capturereagent.

Alternatively, depending on the assay protocol or protocols to be run bythe analyzer 50, the pipette unit 456 may dispense the same testspecimen material into two or more of the receptacle vessels 162 and theanalyzer can perform the same or different assays on each of thosealiquots.

As described above with respect to pipette units 480, 482, pipette unit456 also includes capacitive level sensing capability. The pipette tipsused on the end of the tubular probe 457 are preferably made from aconductive material, so that capacitive level sensing can be performedwith the pipette unit 456, even when a tip is carried on the end of thetubular probe 457. After the pipette unit has completed a test specimendispensing procedure, the pipette unit 456 moves the tubular probe 457back down into the receptacle vessel 162 until the top of the fluidlevel is detected by the change in capacitance. The vertical position ofthe tubular probe 457 is noted to determine whether the proper amount offluid material is contained in the receptacle vessel 162. Lack ofsufficient material in a receptacle vessel 162 can be caused by clottingin the test specimen, which can clot the tip at the end of the tubularprobe 457 and prevent proper aspiration of test specimen material intothe tip and/or can prevent proper dispensing of test specimen from thetip.

After specimen transfer, the pipette tip is discarded into the tipdisposal tube 342 as described above. Again, the tubular probe 457 ofthe pipette of unit can be washed with distilled water if desired, butwashing of the probe is typically not necessary because, in thepreferred method of operation, specimen material only comes into contactwith the disposable pipette tip.

The assay manager program includes pipette unit control logic whichcontrols movements of the pipette units 456, 480, 482, and preferablycauses pipette unit 456 to move in such a manner that it never passesover a specimen tube 320 on the specimen ring 250, except when thepipette unit 456 positions the tubular probe 457 over a specimen tube320 to withdraw a test specimen or when the specimen tube 320 is belowthe plate 138 of the specimen cover. In this way, inadvertent fluiddrips from the tubular probe 457 of the pipette unit 450 into anotherspecimen tube, which might result in cross-contamination, are avoided.

Following specimen preparation, the MTU 160 is moved by the right-sidetransport mechanism 500 from the specimen transfer station to the rightorbital mixer 550 in which the specimen/reagent mixtures are mixed. Thestructure and operation of the orbital mixers 550, 552 will be describedin further detail below.

After the MTU 160 is withdrawn from the specimen transfer station by theright-side transport mechanism 500, the reaction receptacle shuttleassembly within the input queue 150 advances the next MTU into aposition to be retrieved by the right-side transport mechanism 500 whichmoves the next MTU to the specimen transfer station. Specimenpreparation procedures are then repeated for this next MTU.

Transport Mechanisms

The right-side and left-side transport mechanisms 500, 502 will now bedescribed in detail. Referring to FIGS. 13-16, the right-side transportmechanism 500 (as well as the left-side transport mechanism 502) has amanipulating hook member that, in the illustrated embodiment, includesan extendible distributor hook 506 extending from a hook mountingstructure 508 that is radially and slidably displaceable in a slot 510on a plate 512. A housing 504 on top of the plate 512 has an opening 505configured to receive the upper portion of an MTU 160. A stepper motor514 mounted on the plate 512 turns a threaded shaft 516, which, incooperation with a lead screw mechanism, moves the distributor hook 506from the extended position shown in FIGS. 13 and 15, to the retractedposition shown in FIG. 14, the motor 514 and threaded shaft 516constituting elements of a preferred hook member drive assembly. Steppermotor 514 is preferably a modified HSI, series 46000. HSI stepper motorsare available from Haydon Switch and Instrument, Inc. of Waterbury,Conn. The HSI motor is modified by machining the threads off one end ofthe threaded shaft 516, so that the shaft 516 can receive the hookmounting structure 508.

The housing 504, motor 514, and the plate 512 are preferably covered bya conforming shroud 507.

As shown in FIG. 16, a stepper motor 518 turns a pulley 520 via a belt519. (VEXTA stepper motors, model number PK264-01A, available fromOriental Motor Co., Ltd. of Tokyo, Japan, and SDP timing belts, modelnumber A6R51M200060, available from SDP/SI of New Hyde Park, N.Y., arepreferred). Pulley 520 is preferably a custom-made pulley with onehundred sixty-two (162) axial grooves disposed around its perimeter. Amain shaft 522 fixedly attached to the plate 512, by means of auniquely-shaped mounting block 523, extends down through a base 524 andis fixed to the pulley 520. Base 524 is mounted to the datum plate 82 bymeans of mechanical fasteners extending through apertures 525 formedabout the outer periphery of the base 524. A flex circuit 526 providespower and control signals to the hook mounting structure 508 and motor514, while allowing the plate 512 (and the components carried on theplate) to pivot sufficiently so as to rotate as much as 340° withrespect to the base 524. The transport mechanism 500, 502, assemblypreferably includes hard stops (not shown) at either end of the unit'srotational path of travel.

An arm position encoder 531 is preferably mounted on an end of the mainshaft 522. The arm position encoder is preferably an absolute encoder.A2 series encoders from U.S. Digital in Seattle, Wash., model numberA2-S-K-315-H, are preferred.

The assay manager program provides control signals to the motors 518 and514, and to the hook mounting structure 508, to command the distributorhook 506 to engage the MTU manipulating structure 166 on MTU 160. Withthe hook 506 engaged, the motor 514 can be energized to rotate the shaft516 and thereby withdraw the hook 506, and the MTU 160, back into thehousing 504. The MTU 160 is securely held by the transport mechanism500, 502 via the sliding engagement of the connecting rib structure 164of the MTU 160 with opposed edges 511 of plate 512 adjacent slot 510.The plate 512 thereby constitutes an element of a preferred receptaclecarrier assembly that is constructed and arranged to be rotatable aboutan axis of rotation (e.g., the axis of shaft 522) and to receive andcarry a reaction receptacle (e.g., MTU 160). The motor 518 can rotatethe pulley 520 and shaft 522 via the belt 519 to thereby rotate theplate 512 and housing 504 with respect to the base 524. Rotation of thehousing 504 thus changes the orientation of the engaged MTU, therebybringing that MTU into alignment with a different station on theprocessing deck.

Sensors 528, 532 are provided in opposite sides of the housing 504 toindicate the position of the distributor hook 506 within the housing504. Sensor 528 is an end-of-travel sensor, and sensor 532 is a homesensor. Sensors 528, 532 are preferably optical slotted sensorsavailable from Optek Technology, Inc. of Carrollton, Tex., model numberOPB980T11. For the home sensor 532, the sensor beam is broken by a homeflag 536 extending from the hook mounting structure 508 when the hook506 is in its fully retracted position. The beam of the end-of-travelsensor 528 is broken by an end-of-travel flag 534 extending from theopposite side of the hook mounting structure 508 when the hook 506 isfully extended.

An MTU-present sensor 530 mounted in the side of the housing 504 sensesthe presence of an MTU 160 in the housing 504. Sensor 530 is preferablya SUNX, infra-red sensor, available from SUNX/Ramco Electric, Inc., ofWest Des Moines, Iowa.

Temperature Ramping Stations

One or more temperature ramping stations 700 are preferably disposedbelow the jig plate 130 and specimen ring 250 (no temperature rampingstations located below the specimen ring 250 are shown in the figures).After mixing the contents of the MTU 160 within the orbital mixer 550,the right-side transport mechanism 500 may move the MTU 160 from theright orbital mixer 550 to a temperature ramping station 700, dependingon the assay protocol.

The purpose of each ramping station 700 is to adjust the temperature ofan MTU 160 and its contents up or down as desired. The temperature ofthe MTU and its contents may be adjusted to approximate an incubatortemperature before inserting the MTU into the incubator to avoid largetemperature fluctuations within the incubator.

As shown in FIGS. 17-18, a temperature ramping station 700 includes ahousing 702 in which an MTU 160 can be inserted. The housing 702includes mounting flanges 712, 714 for mounting the ramping station 700to the datum plate 82. A thermoelectric module 704 (also known as aPeltier device) in thermal contact with a heat sink structure 706 isattached to the housing 702, preferably at the bottom 710. Preferredthermoelectric modules are those available from Melcor, Inc. of Trenton,N.J., model number CP1.4-127-06L. Although one thermoelectric module 704is shown in FIG. 17, the ramping station 700 preferably includes twosuch thermoelectric modules. Alternatively, the outer surface of thehousing 702 could be covered with a mylar film resistive heating foilmaterial (not shown) for heating the ramping station. Suitable mylarfilm heating foils are etched foils available from Minco Products, Inc.of Minneapolis, Minn. and from Heatron, Inc. of Leavenworth, Kans. Forramp-up stations (i.e., heaters), resistive heating elements arepreferably used, and for ramp-down stations (i.e., chillers),thermoelectric modules 704 are preferably used. The housing 702 ispreferably covered with a thermal insulating jacket structure (notshown).

The heat sink structure used in conjunction with the thermoelectricmodule 704 preferably comprises an aluminum block with heat dissipatingfins 708 extending therefrom.

Two thermal sensors (not shown) (preferably thermistors rated 10 KOhm at25 ° C.) are preferably provided at a location on or within the housing702 to monitor the temperature. YSI 44036 series thermistors availablefrom YSI, Inc. of Yellow Springs, Ohio are preferred. YSI thermistorsare preferred because of their high accuracy and the ±0.1° C.interchangeability provided by YSI thermistors from one thermistor toanother. One of the thermal sensors is for primary temperature control,that is, it sends signals to the embedded controller for controllingtemperature within the ramping station, and the other thermal sensor isfor monitoring ramping station temperature as a back-up check of theprimary temperature control thermal sensor. The embedded controllermonitors the thermal sensors and controls the heating foils or thethermoelectric module of the ramping station to maintain a generallyuniform, desired temperature within the ramping station 700.

An MTU 160 can be inserted into the housing, supported on the MTUsupport flanges 718 which engage the connecting rib structure 164 of theMTU 160. A cut-out 720 is formed in a front edge of a side panel of thehousing 702. The cut-out 720 permits a distributor hook 506 of atransport mechanism 500 or 502 to engage or disengage the MTUmanipulating structure 166 of an MTU 160 inserted all the way into atemperature ramping station 700 by lateral movement with respectthereto.

Rotary Incubators

Continuing with the general description of the assay procedure,following sufficient temperature ramp-up in a ramping station 700, theright-side transport mechanism 500 retrieves the MTU from the rampingstation 700 and places the MTU 160 into the target capture and annealingincubator 600. In a preferred mode of operation of the analyzer 50, thetarget capture and annealing incubator 600 incubates the contents of theMTU 160 at about 60° C. For certain tests, it is important that theannealing incubation temperature not vary more than ±0.5° C. and thatamplification incubation (described below) temperature not vary morethan ±0.1° C. Consequently, the incubators are designed to provide aconsistent uniform temperature.

The details of the structure and operation of the two embodiments of therotary incubators 600, 602, 604 and 606 will now be described. Referringto FIGS. 19-23C, each of the incubators has housing with a generallycylindrical portion 610, suitably mounted to the datum plate 82, withinan insulating jacket 612 and an insulated cover 611.

The cylindrical portion 610 is preferably constructed of nickel-platedcast aluminum and the metal portion of the cover 611 is preferablymachined aluminum. The cylindrical portion 610 is preferably mounted tothe datum plate 82 atop three or more resin “feet” 609. The feet 609 arepreferably formed of Ultem®-1000 supplied by General Electric Plastics.The material is a poor thermal conductor, and therefore the feet 609function to thermally isolate the incubator from the datum plate. Theinsulation 612 and the insulation for the cover 611 are preferablycomprised of ½ inch thick polyethylene supplied by the Boyd Corporationof Pleasantown, Calif.

Receptacle access openings 614, 616 are formed in the cylindricalportion 610, and cooperating receptacle access openings 618, 620 areformed in the jacket 612. For incubators 600 and 602, one of the accessopenings is positioned to be accessible by the right-side transportmechanism 500 and the other access opening is positioned to beaccessible by the left-side transport mechanism 502. Incubators 604 and606 need to be accessible only by the left-side transport mechanism 502and therefore only have a single receptacle access opening.

Closure mechanisms comprising revolving doors 622, 624 are rotatablypositioned within the openings 614 and 616. Each revolving door 622, 624has a MTU slot 626 extending through a solid cylindrical body. The MTUslot 626 is configured to closely match the profile of the MTU 160,having a wider upper portion compared to the lower portion. A doorroller 628, 630 is attached on top of each of the doors 622, 624,respectively. The revolving doors 622, 624 are actuated by solenoids(not shown) which are controlled by commands from the assay managerprogram to open and close the doors 622, 624 at the proper times. A door622 or 624 is opened by turning the door 622, 624 so that the MTU slot626 thereof is aligned with the respective receptacle access opening614, 616 and is closed by turning the door 622, 624 so that the MTU slot626 thereof extends transversely to the respective access opening 614,616. The cylindrical portion 610, cover 611, doors 622, 624, and a floorpanel (not shown) constitute an enclosure which defines the incubationchamber.

The doors 622, 624 are opened to permit insertion or retrieval of an MTUinto or from an incubator and are closed at all other times to minimizeheat loss from the incubator through the access openings 614, 616.

A centrally positioned radial fan 632 is driven by an internal fan motor(not shown). A Papst, model number RER 100-25/14 centrifugal fan,available from ebm/Papst of Farmington, Conn., having a 24VDC motor andrated at 32 cfm is preferred because its shape is well-suited toapplication within the incubator.

Referring now to FIG. 22, an MTU carousel assembly 671 is a preferredreceptacle carrier which carries a plurality of radially oriented,circumferentially-arranged MTUs 160 within the incubator. The MTUcarousel assembly 671 is carried by a top plate 642, which is supportedby the cylindrical portion 610 of the housing, and is preferablyactuated by a rotation motor 640, preferably a stepper motor, supportedat a peripheral edge of on the top plate 642. Rotation motor 640 ispreferably a VEXTA stepper motor, model number PK246-01A, available fromOriental Motor Co., Ltd. of Tokyo, Japan.

The MTU carousel 671 includes a hub 646 disposed below the top plate 642and coupled, via a shaft 649 extending through the top plate 642, to apulley 644. Pulley 644 is preferably a custom-made pulley with onehundred sixty-two (162) axial grooves disposed around its perimeter andis coupled to motor 640 through a belt 643, so that motor 640 can rotatethe hub 646. Belt 643 is preferably a GT® series timing belt availablefrom SDP/SI of New Hyde Park, N.Y. A 9:1 ratio is preferably providedbetween the pulley 644 and the motor 640. The hub 646 has a plurality ofequally spaced-apart internal air flow slots 645 optionally separated byradially-oriented, circumferentially arranged divider walls 647. In theillustration, only three divider walls 647 are shown, although it willbe understood that divider walls may be provided about the entirecircumference of the hub 646. In the preferred embodiment, divider walls647 are omitted. A support disk 670 is attached to hub 646 and disposedbelow top plate 642 in generally parallel relation therewith. Aplurality of radially extending, circumferentially-arranged MTU holdingmembers 672 are attached to the bottom of the support disk 670 (onlythree MTU holding members 672 are shown for clarity). The MTU holdingmembers 672 have support ridges 674 extending along opposite sidesthereof. Radially oriented MTUs are carried on the MTU carousel assembly671 within stations 676 defined by circumferentially adjacent MTUholding members 672, with the support ridges 674 supporting theconnecting rib structures 164 of each MTU 160 carried by the MTUcarousel assembly 671.

The MTU carousel assembly rotates on a carousel drive shaft to which thedrive pulley (644 in the illustrated embodiment) is attached. A carouselposition encoder is preferably mounted on an exterior end of thecarousel drive shaft. The carousel position encoder preferably comprisesa slotted wheel and an optical slot switch combination (not shown). Theslotted wheel can be coupled to the carousel assembly 671 to rotatetherewith, and the optical slot switch can be fixed to the cylindricalportion 610 of the housing or top plate 642 so as to be stationary. Theslotted wheel/slot switch combination can be employed to indicate arotational position of the carousel assembly 671 and can indicate a“home” position (e.g., a position in which an MTU station 676 designatedthe #1 station is in front of the access opening 614). A2 seriesencoders from U.S. Digital in Seattle, Wash., model number A2-S-K-315-H,are preferred.

A heat source is provided in thermal communication with the incubatorchamber defined within the incubator housing comprising the cylindricalportion 610 and cover 611. In the preferred embodiment, Mylarfilm-encased electrically-resistive heating foils 660 surround thehousing 610 and may be attached to the cover 611 as well. Preferredmylar film heating foils are etched foils available from Minco Products,Inc. of Minneapolis, Minn. and Heatron, Inc. of Leavenworth, Kans.Alternative heat sources may include internally mounted resistiveheating elements, thermal-electric heating chips (Peltiers), or a remoteheat-generating mechanism thermally connected to the housing by aconduit or the like.

As shown in FIGS. 19 and 22, a pipette slot 662 extends through theincubator cover 611, radially-aligned pipette holes 663 extend throughthe top plate 642, and pipettes slots 664 are formed in the support disk670 over each MTU station 676, to allow pipetting of reagents into MTUsdisposed within the incubators. In the preferred embodiment of theanalyzer 50 for the preferred mode of operation, only two of theincubators, the amplification incubator 604 and the hybridizationprotection assay incubator 606, include the pipette holes 663 andpipette slots 662 and 664, because, in the preferred mode of operation,it is only in these two incubators where fluids are dispensed into MTUs160 while they are in the incubator.

Two temperature sensors 666, preferably thermistors (10 KOhm at 25° C.),are positioned in the top plate 642. YSI 44036 series thermistorsavailable from YSI, Inc. of Yellow Springs, Ohio are preferred. YSIthermistors are preferred because of their high accuracy and the ±0.1°C. interchangeability provided by YSI thermistors from one thermistor toanother. One of the sensors 666 is for primary temperature control, thatis, it sends singles to the embedded controller for controllingtemperature within the incubator, and the other sensor is for monitoringtemperature of the incubator as a back-up check of the primarytemperature control sensor. The embedded controller monitors the sensors666 and controls the heating foils 660 and fan 632 to maintain auniform, desired temperature within the incubator housing 610.

As a transport mechanism 500, 502 prepares to load an MTU 160 into anincubator 600, 602, 604, or 606, the motor 640 turns the hub 646 tobring an empty MTU station 676 into alignment with the receptacle accessopening 614 (or 616). As this occurs, the door-actuating solenoidcorrespondingly turns the revolving door 622 (or 624) one-quarter turnto align the MTU slot 626 of the door with the MTU station 676. Theaccess opening 614 is thus exposed to allow placement or removal of anMTU 160. The transport mechanism 500 or 502 then advances thedistributor hook 506 from the retracted position to the extendedposition, pushing the MTU 160 out of the housing 504, through the accessopening 614, and into an MTU station 676 in the incubator. After thedistributor hook 506 is withdrawn, the motor 640 turns the hub 646,shifting the previously inserted MTU 160 away from the access opening614, and the revolving door 622 closes once again. This sequence isrepeated for subsequent MTUs inserted into the rotary incubator.Incubation of each loaded MTU continues as that MTU advances around theincubator (counter-clockwise) towards the exit slot 618.

An MTU sensor (preferably an infrared optical reflective sensor) in eachof the MTU stations 676 detects the presence of an MTU 160 within thestation. Optek Technology, Inc. sensors, model number OPB770T, availablefrom Optek Technology, Inc. of Carrollton, Tex. are preferred because ofthe ability of these sensors to withstand the high temperatureenvironment of the incubators and because of the ability of thesesensors to read bar code data fixed to the label-receiving surfaces 175of the label-receiving structures 174 of the MTUs 160. In addition, eachdoor assembly (revolving doors 622, 624) preferably includes slottedoptical sensors (not shown) to indicate door open and door closedpositions. Sensors available from Optek Technology, Inc. of Carrollton,Tex., model number OPB980T11, are preferred because of the relativelyfine resolution provided thereby to permit accurate monitoring of doorposition. A skewed disk linear mixer (also known as a wobbler plate) 634is provided within housing 610 adjacent MTU carousel assembly 671 andoperates as a receptacle mixing mechanism. The mixer 634 comprises adisk mounted in a skewed manner to the shaft of a motor 636 whichextends through opening 635 into the housing 610. The motor ispreferably a VEXTA stepper motor, model number PK264-01A, available fromOriental Motors Ltd. of Tokyo, Japan, which is the same motor preferablyused for the MTU carousel assembly 671. A viscous harmonic damper 638 ispreferably attached to motor 636 to damp out harmonic frequencies of themotor which can cause the motor to stall. Preferred harmonic dampers areVEXTA harmonic dampers, available from Oriental Motors Ltd. Theoperation of the skewed disk linear mixer 634 will be described below.

Only two of the incubators, the amplification incubator 604 and thehybridization protection assay incubator 606, include a skewed disklinear mixer 634, because, in the preferred mode of operation, it isonly in these two incubators where fluids are dispensed into the MTUs160 while they are in the incubator. Thus, it is only necessary toprovide linear mixing of the MTU 160 by the skewed disk linear mixer 634in the amplification incubator 604 and the hybridization protectionassay incubator 606.

To effect linear mixing of an MTU 160 in the incubator by linear mixer634, the MTU carousel assembly 671 moves the MTU 160 into alignment withthe skewed disk linear mixer 634, and the skewed disk of the skewed disklinear mixer 634 engages the MTU manipulating structure 166 of the MTU160. As the motor 636 spins the skewed disk of the skewed disk linearmixer 634, the portion of the skewed disk structure engaged with the MTU160 moves radially in and out with respect to the wall of the housing610, thus alternately engaging the vertical piece 167 of the MTUmanipulating structure 166 and the shield structure 169. Accordingly,the MTU 160 engaged with the skewed disk linear mixer 634 is movedradially in and out, preferably at high frequency, providing linearmixing of the contents of the MTU 160. For the amplification incubationstep of the preferred mode of operation, which occurs within theamplification incubator 604, a mixing frequency of 10 Hz is preferred.For the probe incubation step of the preferred mode of operation, whichoccurs within the hybridization protection assay incubator 606, a mixingfrequency of 14 Hz is preferred. Finally, for the select incubation stepof the preferred mode of operation, which also occurs within thehybridization protection assay incubator 606, a mixing frequency of 13Hz is preferred.

The raised arcuate portions 171, 172 may be provided in the middle ofthe convex surfaces of the vertical piece 167 and the shield structure169 of the MTU 160, respectively, (see FIG. 60) to minimize the surfacecontact between the skewed disk linear mixer 634 and the MTU 160 so asto minimize friction between the MTU 160 and the skewed disk linearmixer 634.

In the preferred embodiment, a sensor is provided at the skewed disklinear mixer 634 to ensure that the skewed disk linear mixer 634 stopsrotating in the “home” position shown in FIG. 21, so that MTUmanipulating structure 166 can engage and disengage from the skewed disklinear mixer 634 as the MTU carousel assembly 671 rotates. The preferred“home” sensor is a pin extending laterally from the skewed disk linearmixer structure and a slotted optical switch which verifies orientationof the skewed disk linear mixer assembly when the pin interrupts theoptical switch beam. Hall effect sensors based on magnetism may also beused.

An alternate MTU carousel assembly and carousel drive mechanism areshown in FIGS. 23A and 23C. As shown in FIG. 23A, the alternateincubator includes a housing assembly 1650 generally comprising acylindrical portion 1610 constructed of nickel-plated cast aluminum, acover 1676 preferably formed of machined aluminum, insulation 1678 forthe cover 1676, and an insulation jacket 1651 surrounding thecylindrical portion 1610. As with the previously described incubatorembodiment, the incubator may include a linear mixer mechanism includinga linear mixer motor 636 with a harmonic damper 638. A closure mechanism1600 (described below) operates to close off or permit access through areceptacle access opening 1614. As with the previously describedembodiment, the incubator may include one or two access openings 1614depending on the location of the incubator and its function within theanalyzer 50.

A centrifugal fan 632 is mounted at a bottom portion of the housing 1650and is driven by a motor (not shown). A fan cover 1652 is disposed overthe fan and includes sufficient openings to permit air flow generated bythe fan 632. A carousel support shaft 1654 includes a lower shaft 1692and an upper shaft 1690 divided by a support disk 1694. The supportshaft 1654 is supported by means of the lower shaft 1692 extending downinto the fan cover 1652 where it is rotatably supported and secured bybearings (not shown).

An MTU carousel 1656 includes an upper disk 1658 having a centralportion 1696. A top surface of the support disk 1694 engages and isattached to a bottom surface of the central portion 1696 of the upperdisk 1658 so that the weight of the carousel 1656 is supported frombelow. As shown in FIG. 23C, a plurality of radially extending,circumferentially spaced station dividers 1660 are attached beneath theupper disk 1658. A lower disk 1662 includes a plurality of radialflanges 1682 emanating from an annular inner portion 1688. The radialflanges 1682 correspond in number and spacing to the carousel stationdividers 1660, and the lower disk 1662 is secured to the bottom surfacesof the carousel station dividers 1660, with each flange 1682 beingsecured to an associated one of the dividers 1660.

The radial flanges 1682 define a plurality of radial slots 1680 betweenadjacent pairs of flanges 1682. As can be appreciated from FIG. 23C, thewidth in the circumferential direction of each flange 1682 at an innerend 1686 thereof is less than the width in the circumferential directionof the flange 1682 at the outer end 1684 thereof. The tapered shape ofthe flanges 1682 ensures that the opposite sides of the slots 1680 aregenerally parallel to one another.

When the lower disk 1662 is attached beneath the carousel stationdividers 1660, the widths of the flanges along at least a portion oftheir respective lengths are greater than the widths of the respectivedividers 1660, which may also be tapered from an outer end thereoftoward an inner end thereof. The flanges 1684 define lateral shelvesalong the sides of adjacent pairs of dividers 1660 for supporting theconnecting rib structure 164 of an MTU 160 inserted into each MTUstation 1663 defined between adjacent pairs of dividers 1660.

A pulley 1664 is secured to the top of the central portion 1696 of theupper disk 1658 and a motor 1672 is carried by a mounting bracket 1670which spans the diameter of the housing 1650 and is secured to thecylindrical portion 1610 of the housing at opposite ends thereof. Themotor is preferably a Vexta PK264-01A stepper motor, and it is coupledto the pulley (having a 9:1 ratio with respect to the motor) by a belt1666, preferably one supplied by the Gates Rubber Company. A positionencoder 1674 is secured to a top central portion of the mounting bracket1672 and is coupled with the upper shaft 1690 of the carousel supportshaft 1654. The encoder 1674 (preferably an absolute encoder of the A2series by U.S. Digital Corporation of Vancouver, Wash.) indicates therotational position of the carousel 1656.

An incubator cover is defined by an incubator plate 1676, preferablyformed of machined aluminum, and a conforming cover insulation element1678. Cover plate 1676 and insulation element 1678 include appropriateopenings to accommodate the encoder 1674 and the motor 1672 and may alsoinclude radial slots formed therein for dispensing fluids into MTUscarried within the incubator as described with regard to the aboveembodiment.

An alternate, and preferred, closure mechanism 1600 is shown in FIG.23B. The cylindrical portion 1610 of the incubator housing includes atleast one receptacle access opening 1614 with outwardly projecting wallportions 1616, 1618 extending integrally from the cylindrical portion1610 along opposite sides of the access opening 1614.

A rotating door 1620 is operatively mounted with respect to the accessopening 1614 by means of a door mounting bracket 1636 attached to thecylindrical portion 1610 of the housing above the access opening 1614.Door 1620 includes an arcuate closure panel 1622 and a transverselyextending hinge plate portion 1628 having a hole 1634 for receiving amounting post (not shown) of the door mounting bracket 1636. The door1622 is rotatable about the opening 1634 with respect to the accessopening 1614 between a first position in which the arcuate closure panel1622 cooperates with the projecting wall portions 1616, 1618 to closeoff the access opening 1614 and a second position rotated outwardly withrespect to the access opening 1614 to permit movement of a receptaclethrough the access opening 1614. An inner arcuate surface of the arcuatepanel 1622 conforms with an arcuate surface 1638 of the door mountingbracket 1636 and an arcuate surface 1619 disposed below the receptacleaccess opening 1614 to permit movement of the arcuate panel 1622 withrespect to the surfaces 1638 and 1619 while providing a minimum gapbetween the respective surfaces so as to minimize heat losstherethrough.

The door 1620 is actuated by a motor 1642 mounted to the incubatorhousing by means of a motor mounting bracket 1640 secured to thecylindrical portion 1610 of the housing beneath the receptacle accessopening 1614. A motor shaft 1644 is coupled to a lower actuating plate1626 of the rotating door 1620 so that rotation of the shaft 1644 istransmitted into rotation of the rotating door 1620. Motor 1642 is mostpreferably an HSI 7.5° per step motor available from Haydon Switch andInstrument, Inc. of Waterbury, Conn. The HSI motor is chosen because ofits relatively low cost and because the closure assembly 1600 does notrequire a high torque, robust motor.

Door position sensors 1646 and 1648 (preferably slotted optical sensors)are operatively mounted on opposite sides of the door mounting bracket1636. The sensor 1646 and 1648 cooperate with sensor tabs 1632 and 1630on the hinge plate 1628 of the door 1620 for indicating the relativeposition of the rotating door 1620 and can be configured so as toindicate, for example, a door open and a door closed status.

A door cover element 1612 is secured to the outside of the cylindricalportion 1610 of the housing so as to cover the door mounting bracket1636 and a portion of the rotating door 1620. The cover element 1612includes an access opening 1613 aligned with the access opening 1614 ofthe incubator housing and further includes a receptacle bridge 1615extending laterally from a bottom edge of the access opening 1613. Thereceptacle bridge 1615 facilitates the insertion of a receptacle (e.g.,an MTU 160) into and withdrawal of the receptacle from the incubator.

While in the target capture and annealing incubator 600, the MTU 160 andtest specimens are preferably kept at a temperature of about 60° C.±0.5°C. for a period of time sufficient to permit hybridization betweencapture probes and target nucleic acids. Under these conditions, thecapture probes will preferably not hybridize with those polynucleotidesdirectly immobilized by the magnetic particles.

Following target capture incubation in the target capture and annealingincubator 600, the MTU 160 is rotated by the incubator carousel to theentrance door 622, also known as the right-side or number onedistributor door. The MTU 160 is retrieved from its MTU station 676within incubator 600 and is then transferred by the right-side transportmechanism 500 to a temperature ramp-down station (not shown) below thespecimen ring 250. In the ramp-down station, the MTU temperature isbrought down to the level of the next incubator. This ramp-down stationthat precedes the active temperature and pre-read cool-down incubator602 is technically a heater, as opposed to a chiller, because thetemperature to which the MTU is decreased, about 40° C., is stillgreater than the ambient analyzer temperature, about 30° C. Accordingly,this ramp-down station preferably uses resistive heating elements, asopposed to a thermoelectric module.

From the ramp-down station, the MTU 160 is transferred by the right-sidetransfer mechanism 500 into the active temperature and pre-readcool-down incubator 602. The design and operation of the activetemperature and pre-read cool-down 602 is similar to that of the targetcapture and annealing incubator 600, as described above, except that theactive temperature and pre-read cool-down incubator 602 incubates at40±1.0° C.

In the AT incubator 602, the hybridization conditions are such that thepolythymidine tail of the immobilized polynucleotide can hybridize tothe polyadenine tail of the capture probe. Provided target nucleic acidhas hybridized with the capture probe in the annealing incubator 600, ahybridization complex can be formed between the immobilizedpolynucleotide, the capture probe and the target nucleic acid in the ATincubator 602, thus immobilizing the target nucleic acid. In the ATincubator 602, the hybridization conditions are such that thepolythymidine tail of the immobilized polynucleotide can hybridize tothe polyadenine tail of the capture probe. Provided target nucleic acidhas hybridized with the capture probe in the annealing incubator 600, ahybridization complex can be formed between the immobilizedpolynucleotide, the capture probe and the target nucleic acid in the ATincubator 602, thus immobilizing the target nucleic acid.

During active temperature binding incubation, the carousel assembly 1656(or 671) of the active temperature and pre-read cool-down incubator 602rotates the MTU to the exit door 624, also known as the number two, orleft-side, distributor door, from which the MTU 160 can be removed bythe left-side transport mechanism 502. The left-side transport mechanism502 removes the MTU 160 from the active temperature and pre-readcool-down incubator 602 and places it into an available magneticseparation wash station 800.

Temperature ramping stations 700 can be a bottle neck in the processingof a number of MTUs through the chemistry deck 200. It may be possibleto use underutilized MTU stations 676 in one or more of the incubatorsin which temperature sensitivity is of less concern. For example, theactive temperature binding process which occurs within the activetemperature and pre-read cool-down incubator 602 at about 40° C. is notas temperature sensitive as the other incubators, and up to fifteen (15)of the incubator's thirty (30) MTU stations 676 may be unused at anygiven time. As presently contemplated, the chemistry deck has only abouteight ramp-up stations, or heaters. Accordingly, significantly more MTUscan be preheated within the unused slots of the active temperature andpre-read cool-down incubator 602 than within the ramp-up stations 700.Moreover, using unused incubator slots instead of heaters allows theomission of some or all of the heaters, thus freeing up space on thechemistry deck.

Magnetic Separation Wash Stations

Turning to FIGS. 24-25, each magnetic separation wash station 800includes a module housing 802 having an upper section 801 and a lowersection 803. Mounting flanges 805, 806 extend from the lower section 803for mounting the magnetic separation wash station 800 to the datum plate82 by means of suitable mechanical fasteners. Locator pins 807 and 811extend from the bottom of lower section 803 of housing 802. Pins 807 and811 register with apertures (not shown) formed in the datum plate 82 tohelp to locate the magnetic separation wash station 800 on the datumplate 82 before the housing 802 is secured by fasteners.

A loading slot 804 extends through the front wall of the lower section803 to allow a transport mechanism (e.g. 502) to place an MTU 160 intoand remove an MTU 160 from the magnetic separation station 800. Atapered slot extension 821 surrounds a portion of the loading slot 804to facilitate MTU insertion through the slot 804. A divider 808separates the upper section 801 from the lower section 803.

A pivoting magnet moving structure 810 is attached inside the lowersection 803 so as to be pivotable about point 812. The magnet movingstructure 810 carries permanent magnets 814, which are positioned oneither side of an MTU slot 815 formed in the magnet moving structure810. Preferably five magnets, one corresponding to each individualreceptacle vessel 162 of the MTU 160, are held in an aligned arrangementon each side of the magnet moving structure 810.

The magnets are preferably made of neodymium-iron-boron (NdFeB), minimumgrade n-35 and have preferred dimensions of 0.5 inch width, 0.3 inchheight, and 0.3 inch depth. An electric actuator, generally representedat 816, pivots the magnet moving structure 810 up and down, therebymoving the magnets 814. As shown in FIG. 25, actuator 816 preferablycomprises a rotary stepper motor 819 which rotates a drive screwmechanism coupled to the magnet moving structure 810 to selectivelyraise and lower the magnet moving structure 810. Motor 819 is preferablyan HSI linear stepper actuator, model number 26841-05, available fromHaydon Switch and Instrument, Inc. of Waterbury, Conn.

A sensor 818, preferably an optical slotted sensor, is positioned insidethe lower section 803 of the housing for indicating the down, or “home”,position of the magnet moving structure 810. Sensor 818 is preferably anOptek Technology, Inc., model number OPB980T11, available from OptekTechnology, Inc. of Carrollton, Tex. Another sensor 817, also preferablyan Optek Technology, Inc., model number OPB980T11, optical slottedsensor, is preferably provided to indicate the up, or engaged, positionof the magnet moving structure 810.

An MTU carrier unit 820 is disposed adjacent the loading slot 804, belowthe divider 808, for operatively supporting an MTU 160 disposed withinthe magnetic separation wash station 800. Turning to FIG. 26, the MTUcarrier unit 820 has a slot 822 for receiving the upper end of an MTU160. A lower fork plate 824 attaches to the bottom of the carrier unit820 and supports the underside of the connecting rib structure 164 ofthe MTU 160 when slid into the carrier unit 820 (see FIGS. 27 and 28). Aspring clip 826 is attached to the carrier unit 820 with its opposedprongs 831, 833 extending into the slot 822 to releasably hold the MTUwithin the carrier unit 820.

An orbital mixer assembly 828 is coupled to the carrier unit 820 fororbitally mixing the contents of an MTU held by the MTU carrier unit820. The orbital mixer assembly 828 includes a stepper motor 830 mountedon a motor mounting plate 832, a drive pulley 834 having an eccentricpin 836, an idler pulley 838 having an eccentric pin 840, and a belt 835connecting drive pulley 834 with idler pulley 838. Stepper motor 830 ispreferably a VEXTA, model number PK245-02A, available from OrientalMotors Ltd. of Tokyo, Japan, and belt 835 is preferably a timing belt,model number A 6G16-170012, available from SDP/SI of New Hyde Park, N.Y.As shown in FIGS. 25 and 26, eccentric pin 836 fits within a slot 842formed longitudinally in the MTU carrier unit 820. Eccentric pin 840fits within a circular aperture 844 formed in the opposite end of MTUcarrier unit 820. As the motor 830 turns the drive pulley 834, idlerpulley 838 also rotates via belt 835 and the MTU carrier unit 820 ismoved in a horizontal orbital path by the eccentric pins 836, 840engaged with the apertures 842, 844, respectively, formed in the carrierunit 820. The rotation shaft 839 of the idler pulley 838 preferablyextends upwardly and has a transverse slot 841 formed therethrough. Anoptical slotted sensor 843 is disposed at the same level as the slot 841and measures the frequency of the idler pulley 838 via the sensor beamintermittently directed through slot 841 as the shaft 839 rotates.Sensor 843 is preferably an Optek Technology, Inc., model numberOPB980T11, sensor, available from Optek Technology, Inc. of Carrollton,Tex.

Drive pulley 834 also includes a locator plate 846. Locator plate 846passes through slotted optical sensors 847, 848 mounted to a sensormounting bracket 845 extending from motor mounting plate 832. Sensors847, 848 are preferably Optek Technology, Inc., model number OPB980T11,sensors, available from Optek Technology, Inc. of Carrollton, Tex.Locator plate 846 has a plurality of circumferentially spaced axialopenings formed therein which register with one or both sensors 847, 848to indicate a position of the orbital mixer assembly 828, and thus aposition of the MTU carrier unit 820.

Returning to FIG. 24, wash buffer solution delivery tubes 854 connect tofittings 856 and extend through a top surface of the module housing 802.Wash buffer delivery tubes 854 extend through the divider 808 viafittings 856, to form a wash buffer delivery network.

As shown in FIGS. 27 and 28, wash buffer dispenser nozzles 858 extendingfrom the fittings 856 are disposed within the divider 808. Each nozzleis located above a respective receptacle vessel 162 of the MTU 160 at alaterally off-center position with respect to the receptacle vessel 162.Each nozzle includes a laterally-directed lower portion 859 fordirecting the wash buffer into the respective receptacle vessel from theoff-center position. Dispensing fluids into the receptacle vessels 162in a direction having a lateral component can limit splashing as thefluid runs down the sides of the respective receptacle vessels 162. Inaddition, the laterally directed fluid can rinse away materials clingingto the sides of the respective receptacle vessels 162.

As shown in FIGS. 24 and 25, aspirator tubes 860 extend through a tubeholder 862, to which the tubes 860 are fixedly secured, and extendthrough openings 861 in the divider 808. A tube guide yoke 809 (see FIG.26) is attached by mechanical fasteners to the side of divider 808,below openings 861. Aspirator hoses 864 connected to the aspirator tubes860 extend to the vacuum pump 1162 (see FIG. 52) within the analyzer 50,with aspirated fluid drawn off into a fluid waste container carried inthe lower chassis 1100. Each of the aspirator tubes 860 has a preferredlength of 12 inches with an inside diameter of 0.041 inches.

The tube holder 862 is attached to a drive screw 866 actuated by a liftmotor 868. Lift motor 868 is preferably a VEXTA, model number PK245-02A,available from Oriental Motors Ltd. of Tokyo, Japan, and the drive screw866 is preferably a ZBX series threaded anti-backlash lead screw,available from Kerk Motion Products, Inc. of Hollis, N.H. The tubeholder 862 is attached to a threaded sleeve 863 of the drive screw 866.Rod 865 and slide rail 867 function as a guide for the tube holder 862.Z-axis sensors 829, 827 (slotted optical sensors) cooperate with a tabextending from threaded sleeve 863 to indicate top and bottom of strokepositions of the aspirator tubes 860. The Z-axis sensors are preferablyOptek Technology, Inc., model number OPB980T11, sensors, available fromOptek Technology, Inc. of Carrollton, Tex.

Cables bring power and control signals to the magnetic separation washstation 800, via a connector 870.

The magnet moving structure 810 is initially in a down position (shownin phantom in FIG. 25), as verified by the sensor 818, when the MTU 160is inserted into the magnetic separation wash station 800 through theinsert opening 804 and into the MTU carrier unit 820. When the magnetmoving structure 810 is in the down position, the magnetic fields of themagnets 814 will have no substantial effect on the magneticallyresponsive particles contained in the MTU 160. In the present context,“no substantial effect” means that the magnetically responsive particlesare not drawn out of suspension by the attraction of the magnetic fieldsof the magnets 814. The orbital mixer assembly 828 moves the MTU carrierunit 820 a portion of a complete orbit so as to move the carrier unit820 and MTU 160 laterally, so that each of the tiplets 170 carried bythe tiplet holding structures 176 of the MTU 160 is aligned with each ofthe aspiration tubes 860, as shown in FIG. 28. The position of the MTUcarrier unit 820 can be verified by the locator plate 846 and one of thesensors 847, 848. Alternatively, the stepper motor 830 can be moved aknown number of steps to place the MTU carrier unit 820 in the desiredposition, and one of the sensors 847, 848 can be omitted.

The tube holder 862 and aspirator tubes 860 are lowered by the liftmotor 868 and drive screw 866 until each of the aspirator tubes 860frictionally engages a tiplet 170 held in an associated carryingstructure 176 on the MTU 160.

As shown in FIG. 25A, the lower end of each aspirator tube 860 ischaracterized by a tapering, step construction, whereby the tube 860 hasa first portion 851 along most of the extent of the tube, a secondportion 853 having a diameter smaller than that of the first portion851, and a third portion 855 having a diameter smaller than that of thesecond portion 853. The diameter of the third portion 855 is such as topermit the end of the tube 860 to be inserted into the flared portion181 of the through hole 180 of the tiplet 170 and to create aninterference friction fit between the outer surface of third portion 855and the two annular ridges 183 (see FIG. 59) that line the inner wall ofhole 180 of tiplet 170. An annular shoulder 857 is defined at thetransition between second portion 853 and third portion 855. Theshoulder 857 limits the extent to which the tube 860 can be insertedinto the tiplet 170, so that the tiplet can be stripped off after use,as will be described below.

The tiplets 170 are at least partially electrically conductive, so thatthe presence of a tiplet 170 on an aspirator tube 860 can be verified bythe capacitance of a capacitor comprising the aspirator tubes 860 as onehalf of the capacitor and the surrounding hardware of the magneticseparation wash station 800 as the other half of the capacitor. Thecapacitance will change when the tiplets 170 are engaged with the endsof the aspirator tubes 860.

In addition, five optical slotted sensors (not shown) can bestrategically positioned above the divider 808 to verify the presence ofa tiplet 170 on the end of each aspirator tube 860. Preferred“tiplet-present” sensors are Optek Technology, Inc., model numberOPB930W51, sensors, available from Optek Technology, Inc. of Carrollton,Tex. A tiplet 170 on the end of an aspirator tube 860 will break thebeam of an associated sensor to verify presence of the tiplet 170. If,following a tiplet pick-up move, tiplet engagement is not verified bythe tiplet present sensors for all five aspirator tubes 860, the MTU 160must be aborted. The aborted MTU is retrieved from the magneticseparation wash station 800 and sent to the deactivation queue 750 andultimately discarded.

After successful tiplet engagement, the orbital mixer assembly 828 movesthe MTU carrier unit 820 back to a fluid transfer position shown in FIG.27 as verified by the locator plate 846 and one or both of the sensors847, 848.

The magnet moving structure 810 is then raised to the up position shownin FIG. 24 so that the magnets 814 are disposed adjacent opposite sidesof the MTU 160. With the contents of the MTU subjected to the magneticfields of the magnets 814, the magnetically responsive particles boundindirectly to the target nucleic acids will be drawn to the sides of theindividual receptacle vessels 162 adjacent the magnets 814. Theremaining material within the receptacle vessels 162 should besubstantially unaffected, thereby isolating the target nucleic acids.The magnet moving structure 810 will remain in the raised position foran appropriate dwell time, as defined by the assay protocol andcontrolled by the assay manager program, to cause the magnetic particlesto adhere to the sides of the respective receptacle vessels 162.

The aspirator tubes are then lowered into the receptacle vessels 162 ofthe MTU 160 to aspirate the fluid contents of the individual receptaclevessels 162, while the magnetic particles remain in the receptaclevessels 162, adhering to the sides thereof, adjacent the magnets 814.The tiplets 170 at the ends of the aspirator tubes 860 ensure that thecontents of each receptacle vessel 162 do not come into contact with thesides of the aspirator tubes 860 during the aspirating procedure.Because the tiplets 170 will be discarded before a subsequent MTU isprocessed in the magnetic separation wash station 800, the chance ofcross-contamination by the aspirator tubes 860 is minimized.

The electrically conductive tiplets 170 can be used in a known mannerfor capacitive fluid level sensing within the receptacle vessels 162 ofthe MTUs. The aspirator tubes 860 and the conductive tiplets 170comprise one half of a capacitor, the surrounding conductive structurewithin the magnetic separation wash station comprises the second half ofthe capacitor, and the fluid medium between the two halves of thecapacitor constitutes the dielectric. Capacitance changes due to achange in the nature of the dielectric can be detected.

The capacitive circuitry of the aspirator tubes 860 can be arranged sothat all five aspirator tubes 860 operate as a single gang level-sensingmechanism. As a gang level-sensing mechanism, the circuitry will onlydetermine if the fluid level in any of the receptacle vessels 162 ishigh, but cannot determine if the fluid level in one of the receptaclevessels is low. In other words, when any of the aspirator tubes 860 andits associated tiplet 170 contacts fluid material within a receptaclevessel, capacitance of the system changes due to the change in thedielectric. If the Z-position of the aspirator tubes 860 at which thecapacitance change occurs is too high, then a high fluid level in atleast one receptacle vessel is indicated, thus implying an aspirationfailure. On the other hand, if the Z-position of the aspirator tubes atwhich the capacitance change occurs is correct, the circuitry cannotdifferentiate between aspirator tubes, and, therefore, if one or more ofthe other tubes has not yet contacted the top of the fluid, due to a lowfluid level, the low fluid level will go undetected.

Alternatively, the aspirator tube capacitive circuitry can be arrangedso that each of the five aspirator tubes 860 operates as an individuallevel sensing mechanism.

With five individual level sensing mechanisms, the capacitive levelsensing circuitry can detect failed fluid aspiration in one or more ofthe receptacle vessels 162 if the fluid level in one or more of thereceptacle vessels is high. Individual capacitive level sensingcircuitry can detect failed fluid dispensing into one or more of thereceptacle vessels 162 if the fluid level in one or more of thereceptacle vessels is low. Furthermore, the capacitive level sensingcircuitry can be used for volume verification to determine if the volumein each receptacle vessel 162 is within a prescribed range. Volumeverification can be performed by stopping the descent of the aspiratortubes 860 at a position above expected fluid levels, e.g. 110% ofexpected fluid levels, to make sure none of the receptacle vessels has alevel that high, and then stopping the descent of the aspirator tubes860 at a position below the expected fluid levels, e.g. 90% of expectedfluid levels, to make sure that each of the receptacle vessels has afluid level at least that high.

Following aspiration, the aspirator tubes 860 are raised, the magnetmoving structure 810 is lowered, and a prescribed volume of wash bufferis dispensed into each receptacle vessel 162 of the MTU 160 through thewash buffer dispenser nozzles 858. To prevent hanging drops of washbuffer on the wash buffer dispenser nozzles 858, a brief,post-dispensing air aspiration is preferred.

The orbital mixer assembly 828 then moves the MTU carriers 820 in ahorizontal orbital path at high frequency to mix the contents of the MTU160. Mixing by moving, or agitating, the MTU in a horizontal plane ispreferred so as to avoid splashing the fluid contents of the MTU and toavoid the creation of aerosols. Following mixing, the orbital mixerassembly 828 stops the MTU carrier unit 820 at the fluid transferposition.

To further purify the targeted nucleic acids, the magnet movingstructure 810 is again raised and maintained in the raised position fora prescribed dwell period. After magnetic dwell, the aspirator tubes 860with the engaged tiplets 170 are lowered to the bottoms of thereceptacle vessels 162 of the MTU 160 to aspirate the test specimenfluid and wash buffer in an aspiration procedure essentially the same asthat described above.

One or more additional wash cycles, each comprising a dispense, mix,magnetic dwell, and aspirate sequence, may be performed as defined bythe assay protocol. Those skilled in the art of nucleic acid-baseddiagnostic testing will be able to determine the appropriate magneticdwell times, number of wash cycles, wash buffers, etc. for a desiredtarget capture procedure.

While the number of magnetic separation wash stations 800 can vary,depending on the desired throughput, analyzer 50 preferably includesfive magnetic separation wash stations 800, so that a magneticseparation wash procedure can be performed on five different MTUs inparallel.

After the final wash step, the magnet moving structure 810 is moved tothe down position and the MTU 160 is removed from the magneticseparation wash station 800 by the left-side transport mechanism 502 andis then placed into the left orbital mixer 552.

After the MTU 160 is removed from the wash station, the tiplets 170 arestripped from the aspiration tubes 860 by a stripper plate 872 locatedat the bottom of the lower section 803 of the housing 802.

The stripper plate 872 has a number of aligned stripping holes 871corresponding in number to the number of aspiration tubes 860, which isfive in the preferred embodiment. As shown in FIGS. 29A to 29D, eachstripping hole 871 includes a first portion 873, a second portion 875smaller than first portion 873, and a bevel 877 surrounding portions 873and 875. The stripper plate 872 is oriented in the bottom of the housing802 so that the small portion 875 of each stripping hole 871 isgenerally aligned with each associated aspiration tube 860, as shown inFIG. 29A. The aspiration tubes 860 are lowered so that the tiplet 170 atthe end of each aspirator tube 860 engages the stripping hole 871. Smallportion 875 is too small to accommodate the diameter of a tiplet 170, sothe bevel 877 directs the tiplet 170 and the aspirator tube 860 towardthe larger portion 873, as shown in FIG. 29B. The aspirator tubes 860are made of an elastically flexible material, preferably stainlesssteel, so that, as the aspirator tubes 860 continue to descend, thebeveled portion 877 causes each of aspirator tubes 860 to deflectlaterally. The small portion 875 of the stripping hole 871 canaccommodate the diameter of the aspirator tube 860, so that after therim 177 of the tiplet 170 clears the bottom of stripping hole 871, eachof the aspirator tubes 860 snaps, due to its own resilience, into thesmall portion 875 of the stripping hole 871 as shown in FIG. 29C. Theaspirator tubes 860 are then raised, and the rim 177 of each tiplet 170engages the bottom peripheral edge of the small portion 875 of strippinghole 871. As the aspirator tubes 860 ascend further, the tiplets 170 arepulled off the aspirator tubes 860 by the stripping holes 871 (see FIG.29D). The stripped tiplets 170 are directed by a chute into a solidwaste container, such as the tiplet waste bin 1134.

The capacitance of the aspiration tubes 860 is sampled to verify thatall tiplets 170 have been stripped and discarded. The stripping step canbe repeated if necessary.

An alternate stripper plate 882 is shown in FIGS. 31A to 31C. Stripperplate 882 includes a number of stripping holes 881 corresponding to thenumber of aspirator tubes 860, which is five in the preferredembodiment. Each stripping hole 881 includes a through-hole 883surrounded by a bevelled countersink 887. A pair of tangs 885 extendlaterally from diametrically opposed positions below the through-hole883. Tangs 885 are preferably made from a spring steel and include av-notch 886 at their ends.

As an aspirator tube 860 with a tiplet 170 disposed on its end islowered toward stripping hole 881, bevelled portion 887 ensures that anymisaligned tubes are directed into the through-hole 883. The spacingbetween the ends of the opposed tangs 885 is less than the diameter ofthe tiplet 170, so as the aspirator tube 860 and tiplet 170 are lowered,the tiplet engages the tangs 885, causing them to deflect downwardly asthe tiplet 170 is forced between tangs 885. When the aspirator tubes 860are raised, the notches 886 of the tangs 885 grip the relatively softmaterial of the tiplet 170, thus preventing upward relative movement ofthe tiplet 170 with respect to the tangs 885. As the tubes continue toascend, the tangs 885 pull the tiplet 170 off the tube 860. When theaspirator tubes 860 are subsequently lowered to strip a subsequent setof tiplets, the tiplet held between the tangs from the previousstripping is pushed through the tangs by the next tiplet and is directedtoward waste bin 1134 (see FIG. 52) located in the lower chassis 1100generally below the five magnetic separation wash stations 800.

Still another alternate, and the presently preferred, stripper plate1400 is shown in FIGS. 30A-30D. Stripper plate 1400 includes fivestripper cavities 1402, each including an initial frusto-conical portion1404. The frusto-conical portion 1404 tapers down to a neck portion 1406which connects to an enlarged straight section 1408. Straight section1408 is offset with respect to the center of neck portion 1406, so thatone side of the straight section 1408 is flush with a side of the neckportion 1406, and an opposite side of the straight section 1408 isoffset from and undercuts the side of the neck portion 1406, therebyforming a ledge 1414. Following the straight section 1408, a slopedportion 1410 is provided on a side of the stripper cavity 1402 oppositethe ledge 1414. Sloped portion 1410 tapers inwardly toward a bottomopening 1412.

As an aspirator tube 860 with a tiplet 170 on its end is moved towardthe stripper cavity 1402, the frusto-conical portion 1404 directs thetiplet 170 and tube 860 toward the neck portion 1406. The aspirator tube860 continues to descend, and the tiplet 170 enters the straight section1408 as the rim 177 of the tiplet 170 clears the bottom of thefrusto-conical portion 1404 and passes through the neck portion 1406.

If the aspirator tube 860 and the stripper cavity 1402 are in proper,preferred alignment, a portion of the rim 177 of the tiplet 170 will bedisposed below the ledge 1414 of the stripper cavity 1402 when thetiplet 170 has moved through the neck portion 1406 and into the straightsection 1408. To ensure that a portion of the rim 177 will be disposedbeneath the ledge 1414, the tiplet 170 engages the lower sloped portion1410 as the aspirator tube 860 descends further to urge the aspiratortube laterally to direct the tiplet 170 below the ledge 1414.

The annular shoulder 857 (see FIG. 25A) formed at the bottom of theaspirator tube 860 ensures that the tube 860 is not forced further intothe through hole 180 of the tiplet 170 as the tube 860 is lowered intothe stripper cavity 1402. The aspirator tube 860 then ascends, and theledge 1414 catches the rim 177 and strips the tiplet 170 off the tube860. The stripped tiplet 170 falls through bottom opening 1412 and intothe waist bin 1134 in the lower chassis 1100 (see FIG. 52).

With each of the stripper plates described above, the position of thetiplet-stripping elements are not all the same. For example, the ledges1414 of the stripper cavities 1402 of the stripper plate 1400 are not atthe same height throughout all the cavities. Preferably, threetiplet-stripping elements are at one height, and two tiplet-strippingelements are at a slightly different height above or below the otherthree elements. The result of the offset tiplet-stripping elements isthat the static friction of the tiplet 170 on the end of the aspiratortube 860 need not be overcome, or broken, for all five tubes 860 atonce. As the aspirator tubes 860 begin to ascend, static friction of thetiplets 170 is broken for one set (two or three) of aspirator tubes 860first, and then, as the tubes 860 continue to ascend, static friction ofthe tiplets 170 is broken for the remaining tubes 860. By not breakingstatic friction of the tiplets 170 for all five aspirator tubes 860 atonce, the loads to which the tube holder 862, drive screw 866, threadedsleeve 863, and lift motor 868 are subjected are kept to a lower level.

Orbital Mixers

The left orbital mixer 552 (and the right orbital mixer 550), as shownin FIGS. 32-34, are constructed and operate in the same manner as thelower housing section 803 and the orbital mixer assembly 828 of themagnetic separation wash stations 800 described above. Specifically, theorbital mixer 550 (552) includes a housing 554, including a front plate551, a back plate 559, and mounting flanges 555, 556, for mounting theorbital mixer 550 (552) to the datum plate 82. An insert opening 557 isformed in a front edge of the housing 554. An MTU carrier 558 has a forkplate 560 attached to the bottom thereof and an MTU-retaining clip 562attached to a back portion of the carrier 558 with opposed prongs of theclip 562 extending into an inner cavity of the carrier 558 thataccommodates the MTU. An orbital mixer assembly 564 includes a drivemotor 566 mounted to a motor mounting plate 567, a drive wheel 568having an eccentric pin 570, an idler wheel 572 having an eccentric pin573, and a belt 574. Drive motor 566 is preferably a stepper motor, andmost preferably a VEXTA, model number PK245-02A, available from OrientalMotors Ltd. of Tokyo, Japan. Belt 574 is preferably a timing belt, modelnumber A 6G16-170012, available from SDP/SI of New Hyde Park, N.Y. Theorbital mixer assembly 564 is coupled to the MTU carrier 558 through theeccentric pins 570, 573 to move the MTU carrier 558 in an orbital pathto agitate the contents of the MTU. The drive wheel 568 includes alocator plate 576, which, in conjunction with sensor 578 attached tosensor mounting bracket 579, verifies the proper positioning of the MTUcarrier 558 for inserting an MTU 160 into the orbital mixer 552 (550)and retrieving an MTU 160 from the orbital mixer. Sensor 578 ispreferably an Optek Technology, Inc., model number OPB980T11, sensor,available from Optek Technology, Inc. of Carrollton, Tex.

A top plate 580 is attached atop housing 554. Top plate 580 of the leftorbital mixer 552 includes a number of tube fittings 582, preferablyfive, to which are coupled a like number of flexible delivery tubes (notshown) for delivering a fluid from a bulk fluid container to an MTU 160located within the mixer via dispenser nozzles 583. Top plate 580 alsoincludes a plurality of pipette openings 581, corresponding in number tothe number of individual receptacle vessels 162 comprising a single MTU160, which is preferably five.

With the MTU 160 held stationary in the left orbital mixer 552, pipetteunit 480 of the left pipette assembly 470 transfers a prescribed volumeof amplification reagent from a container within the reagent cooling bay900 into each receptacle vessel 162 of the MTU 160 through the pipetteopenings 581. The amplification reagent used will depend upon theamplification procedure being followed. Various amplification proceduresare well known to those skilled in the art of nucleic acid-baseddiagnostic testing, a number of which are discussed in the backgroundsection above.

Next, the contents of the MTU are mixed by the orbital mixer assembly564 of the orbital mixer 552 to ensure proper exposure of the targetnucleic acid to amplification reagent. For a desired amplificationprocedure, those skilled in the art of nucleic acid-based diagnostictesting will be able to determine the appropriate components and amountsof an amplification reagent, as well as mix frequencies and durations.

After pipetting amplification reagent into the MTU 160, the pipette unit480 is moved to a rinse basin (described below) on the processing deck200, and pipette unit 480 is washed by running distilled water throughprobe 481. The distilled water is pumped from bottle 1140 in the lowerchassis 1100, and the purge water is collected in a liquid wastecontainer 1128 in the lower chassis 1100.

After mixing the contents of the MTU 160, a layer of silicon oil isdispensed into each receptacle vessel through the dispenser nozzles 583.The layer of oil, pumped from bottles 1168 in the lower chassis 1100,helps prevent evaporation and splashing of the fluid contents of the MTU160 during subsequent manipulation and incubation of the MTU 160 and itscontents.

Reagent Cooling Bay

The reagent cooling bay 900 will now be described.

Referring to FIGS. 35-39, the reagent cooling bay 900 includes aninsulating jacket 902 fitted around a cylindrical housing 904,preferably made from aluminum. A cover 906, preferably made of Delrin,sits atop housing 904 with a registration tab 905 of cover 906 fittingwithin slot 907 in housing 904 to ensure proper orientation of the cover906 An optical sensor may be provided proximate to or within slot 907for verifying that tab 905 is seated within slot 907. Alternatively, anoptical sensor assembly 909 can be secured to an edge of an upper rim ofthe housing 904 for verifying cover placement. The optical sensorassembly 909 cooperates with a sensor-tripping structure (not shown) onthe cover 906 to verify that the cover is in place. Optical sensorassembly 909 preferably includes an Optek Technology, Inc. slottedoptical sensor, model number OPB980T11, available from Optek Technology,Inc. of Carrollton, Tex. The cover 906 also includes pipette openings908 through which pipette units 480, 482 can access reagent containerswithin the cooling bay 900.

The housing 904 is attached to a floor plate 910, and the floor plate910 is attached to the datum plate 82 by means of suitable mechanicalfasteners extending through openings formed in mounting flanges 911spaced about the periphery of the floor plate 910. Cooling units 912,preferably two, are attached to floor plate 910. Each cooling unit 912comprises a thermoelectric module 914 attached cool-side-up to thebottom surface of floor plate 910. Thermoelectric modules available fromMelcor, Inc. of Trenton, N.J., model number CP1.4-127-06L, provide thedesired cooling capacity. A heat sink 916, including a plurality ofheat-dissipating fins 915, is attached to, or may be integral with, thebottom surface of floor plate 910, directly below the thermoelectricmodule 914. A fan unit 918 is attached in a position to drain heat awayfrom heat sink 916. Fan units 918 are preferably Orix fans, model numberMD825B-24, available from Oriental Motors Ltd. of Tokyo, Japan.Together, the cooling units 912 cool the interior of the housing 904 toa prescribed temperature for the benefit of temperature-sensitivereagents (e.g., enzymes) stored within the bay 900.

Two temperature sensors (only one temperature sensor 920 is shown) aredisposed within the cooling bay 900 housing 904 for monitoring andcontrolling the interior temperature thereof. The temperature sensorsare preferably thermistors (10 KOhm at 25° C.), and YSI 44036 seriesthermistors available from YSI, Inc. of Yellow Springs, Ohio are mostpreferred. YSI thermistors are preferred because of their high accuracyand the ±0.1° C. interchangeability provided by YSI thermistors from onethermistor to another. One of the sensors is a primary temperaturecontrol sensor, and the other is a temperature monitoring sensor. On thebasis of the temperature indications from the primary control sensor,the embedded controller adjusts power to the thermoelectric modules 914and/or power to the fan units 918 to control cooling bay temperature.The temperature monitoring sensor provides a verification check of theprimary temperature control sensor.

As shown in FIG. 38, container tray 922 is a one-piece turntablestructure with bottle-holding cavities 924 sized and shaped to receiveand hold specific reagent bottles 925. A drive system for container tray922 includes a motor 926, a small pulley 931 on the shaft of motor 926,a belt 928, a pulley 930, and a shaft 932. (a VEXTA stepper motor, modelnumber PK265-02A, available from Oriental Motor Co., Ltd. of Tokyo,Japan, and an SDP timing belt, GT® Series, available from SDP/SI of NewHyde Park, N.Y., are preferred). Motor 926 and cooling units 912 extendthrough openings (not shown) formed in the datum plate 82 and extendbelow the floor plate 910.

Container tray 922 may include a central, upstanding handle 923 tofacilitate installation of the tray 922 into and removal of the tray 922from the housing 904. A top portion 933 of shaft 932 extends throughfloor plate 910 and is received by a mating aperture (not shown) formedin the bottom of the tray 922. A sensor 940 extending up through thefloor plate 910 and into the housing 904 verifies that tray 922 is inplace within the housing 904. Sensor 940 is preferably a capacitiveproximity sensor available from Advanced Controls, Inc., of Bradenton,Fla., model number FCP2.

A position encoder 934 (preferably a slotted disk) in conjunction withan optical sensor 935 may be used to detect the position of thecontainer tray 922, so that a specific reagent bottle 925 may be alignedunder the pipette openings 908 in the cover 906.

As shown in FIG. 37, a preferred alternative to the position encoder 934and optical sensor 935 includes four slotted optical sensors 937 (onlytwo sensors are visible in FIG. 36) provided inside the housing 904along with a flag pin (not shown) extending from the bottom of containertray 922. One sensor is provided for each quadrant of the container tray922, and the flag trips one of the four sensors to indicate whichquadrant of the container tray 922 is aligned with the pipette openings908. Sensors 937 are preferably Optek Technology, Inc. sensors, modelnumber OPB98OT11, available from Optek Technology, Inc. of Carrollton,Tex.

A preferred alternative to the one-piece container tray 922 shown inFIG. 38 is a modular tray 1922 shown in FIGS. 35 and 39. Tray 1922includes a circular base plate 1926 and an upstanding handle post 1923attached to a central portion thereof. Modular pieces 1930 havingbottle-holding cavities 1924 are preferably connected to one another andto the base plate 1926 by pins 1928 and screws (not shown) to form thecircular tray 1922. Other means of securing the modular pieces 1930 maybe employed in the alternative to pins 1928 and screws. The modularpieces 1930 shown in the figures are quadrants of a circle, and thus, ofcourse, four such pieces 1930 would be required to complete the tray1922. Although quadrants are preferred, the modular pieces may howeverbe sectors of various sizes, such as, for example, ½ of a circle or ⅛ ofa circle.

Alphanumeric bottle location labels 1940 are preferably provided on thebase plate 1926 to identify positions within the tray 1922 for reagentcontainers. The preferred label scheme includes an encircledletter-number pair comprising a leading letter A, E, P, or S with atrailing number 1, 2, 3, or 4, The letters A, E, P, and S, designateamplification reagent, enzyme reagent, probe reagent, and selectreagent, respectively, corresponding to the preferred mode of use of theanalyzer 50, and the numbers 1-4 designate a quadrant of the tray 1922.Each modular piece 1930 includes a circular hole 1934 at the bottom ofeach bottle-holding cavity 1924. The holes 1934 align with the bottlelocation labels 1940, so that the labels 1940 can be seen when themodular pieces 1930 are in place on the base plate 1926.

The modular pieces 1930 of the container tray 1922 are configured toaccommodate reagent containers of different sizes corresponding toreagent quantities sufficient for performing two hundred fifty (250)assays or reagent quantities sufficient for performing five hundred(500) assays. Four 250-assay modular quadrants permit the reagentcooling bay to be stocked for 1000 assays, and four 500-assay modularquadrants permit the reagent cooling bay to be stocked for 2000 assays.Modular quadrants for 250 or 500 assay reagent kits can be mixed andmatched to configure the container tray for accommodating variousnumbers of a single assay type or various numbers of multiple differentassay types.

An insulation pad 938 is disposed between the container tray 922 and thefloor plate 910. Power, control, temperature, and position signals areprovided to and from the reagent cooling bay 900 by a connector 936 anda cable (not shown) linked to the embedded controller of the analyzer50.

A bar code scanner 941 is mounted to an upstanding scanner mountingplate 939 attached to floor plate 910 in front of an opening 942 formedin a side-wall of the cooling bay 900. The bar code scanner 941 is ableto scan bar code information from each of the reagent containers carriedon the container tray 922. As shown in FIG. 39, longitudinal slots 1932are formed along the bottle-holding cavities 1924, and bar codeinformation disposed on the sides of the reagent container held in thebottle-holding cavities 1924 can be align with the slots 1932 to permitthe bar code scanner 941 to scan the bar code information. A preferredbar code scanner is available from Microscan of Newbury Park, Calif.under model number FTS-0710-0001.

Pipette rinse basins 1942, 1944 are attached to the side of the housing904. Each rinse basin 1942, 1944 provides an enclosure structure with aprobe-receiving opening 1941, 1945, respectively, formed in a top panelthereof and a waste drain tube 1946, 1948, respectively, connected to abottom portion thereof. A probe of a pipette unit can be inserted intothe rinse basin 1942, 1944 through the probe-receiving opening 1941,1945, and a wash and/or rinse fluid can be passed through the probe andinto the basin. Fluid in the rinse basin 1942, 1944 is conducted by therespective waste drain tube 1946, 1948 to the appropriate waste fluidcontainer in the lower chassis 1100. In the preferred arrangement andmode of operation of the analyzer 50, probe 481 of pipette unit 480 isrinsed in rinse basin 1942, and probe 483 of pipette unit 482 is rinsedin rinse basin 1944.

After the amplification reagent and oil are added to the receptaclevessels 162 of MTU 160 in the left orbital mixer 552, the left-sidetransport mechanism 502 retrieves the MTU 160 from the left orbitalmixer 552 and moves the MTU 160 to an available temperature ramp-upstation 700 that is accessible to the left-side transport mechanism 502,i.e. on the left side of the chemistry deck 200, to increase thetemperature of the MTU 160 and its contents to about 60° C.

After sufficient ramp-up time in the ramp-up station 700, the left-sidetransport mechanism 502 then moves the MTU 160 to the target capture andannealing incubator 600. The left-side distributor door 624 of thetarget capture and annealing incubator 600 opens, and the MTU carouselassembly 671 within the incubator 600 presents an empty MTU station 676to permit the left-side transport mechanism to insert the MTU into theincubator 600. The MTU 160 and its contents are then incubated at about60° C. for a prescribed incubation period. During incubation, the MTUcarousel assembly 671 may continually rotate within the incubator 600 asother MTUs 600 are removed from and inserted into the incubator 600.

Incubating at 60° C. in the annealing incubator 600 permits dissociationof the capture probe/target nucleic acid hybridization complex from theimmobilized polynucleotide present in the assay solution. At thistemperature, oligonucleotide primers introduced from the reagent coolingbay 900 can hybridize to the target nucleic acid and subsequentlyfacilitate amplification of the target nucleotide base sequence.

Following incubation, the MTU carousel assembly 671 within incubator 600rotates the MTU 160 to the left-side distributor door 624, the left sidedistributor door 624 opens, and the left-side transport mechanism 502retrieves the MTU 160 from the MTU carousel assembly 671 of the targetcapture and annealing incubator 600. The left-side transport mechanism502 then moves the MTU 160 to, and inserts the MTU 160 into, anavailable temperature ramp-down station 700 that is accessible to theleft-side transport mechanism 502. The temperature of the MTU 160 andits contents is decreased to about 40° C. in the ramp-down station. TheMTU 160 is then retrieved from the ramp-down station by the left-sidetransport mechanism 502 and is moved to the active temperature andpre-read cool-down incubator 602. The left-side distributor door 624 ofthe AT incubator 602 opens, and the MTU carousel assembly 671 withinincubator 602 presents an empty MTU station 676, so that the left-sidetransport mechanism 502 can insert the MTU into the incubator 602.Within the active temperature and pre-read cool-down incubator 602, theMTU is incubated at about 41° C. for a period of time necessary tostabilize the temperature of the MTU.

From the active temperature and pre-read cool-down incubator 602, theMTU is moved by transport mechanism 502 to the amplification incubator604 in which the temperature of the MTU is stabilized at 41.5° C. TheMTU carousel assembly 671 within the amplification incubator 604 rotatesto place the MTU at the pipetting station below the pipette openings 662formed in the cover 611 (see, e.g., FIG. 19). The container tray 922within the reagent cooling bay 900 rotates to place the enzyme reagentcontainer below a pipette opening 908, and pipette unit 482 of pipetteassembly 470 transfers enzyme reagent from the reagent cooling bay 900to each of the receptacle vessels 162 of the MTU 160.

As explained above, pipette units 480, 482 use capacitive level sensingto ascertain fluid level within a container and submerge only a smallportion of the end of the probe 481, 483 of the pipette unit 480, 482 topipette fluid from the container. Pipette units 480, 482 preferablydescend as fluid is drawn into the respective probe 481, 483 to keep theend of the probe submerged to a constant depth. After pipetting reagentinto the pipette unit 480 or 482, the pipette unit creates a minimumtravel air gap of 10 μl in the end of the respective probe 481 or 483 toensure no drips fall from the end of the probe.

After enzyme reagent is added to each receptacle vessel 162, the MTUcarousel assembly 671 of amplification incubator 604 rotates MTU 160 tothe skewed disk linear mixer 634 within amplification incubator 604 andthe MTU 160 and its contents are mixed as described above at about 10 Hzto facilitate exposure of the target nucleic acid to the added enzymereagent. The pipette unit 482 is moved to rinse basin 1942, and theprobe 483 is rinsed by passing distilled water through it.

The MTU 160 is then incubated within amplification incubator 604 atabout 41.5° C. for a prescribed incubation period. The incubation periodshould be sufficiently long to permit adequate amplification of at leastone target nucleotide base sequence contained in one or more targetnucleic acids which may be present in the receptacle tubes 162. Althoughthe preferred embodiment is designed to facilitate amplification using atranscription-mediated amplification (TMA) procedure, which is discussedin the background section supra, practitioners will easily appreciatethose modifications necessary to perform other amplification proceduresusing the analyzer 50. In addition, an internal control sequence ispreferably added at the beginning of the assay to provide confirmationthat the amplification conditions and reagents were appropriate foramplification. Internal controls are well known in the art and requireno further discussion here.

Following amplification incubation, the MTU 160 is moved by theleft-side transport mechanism 502 from the amplification incubator 604to an available ramp-up station 700 that is accessible to the left-sidetransport mechanism 502 to bring the temperature of the MTU 160 and itscontents to about 60° C. The MTU 160 is then moved by the left-sidetransport mechanism 502 into the hybridization incubator 606. The MTU160 is rotated to a pipetting station in the hybridization incubator606, and a probe reagent from the reagent cooling bay 900 is pipettedinto each receptacle vessel, through openings 662 in the cover 611 ofthe hybridization incubator 606, by the pipette unit 480. The probereagent includes chemiluminescent detection probes, and preferablyacridinium ester (AE)-labeled probes which can be detected using ahybridization protection assay (HPA). Acridinium ester-labeled probesand the HPA assay are well known in the art and are described more fullyin the background section supra. While AE-labeled probes and the HPAassay are preferred, the analyzer 50 can be conveniently adapted toaccommodate a variety of detection methods and associated probes, bothlabeled and unlabeled. Confirmation that detection probe has been addedto the receptacle vessels 162 can be accomplished using an internalcontrol that is able (or its amplicon is able) to hybridize to a probein the probe reagent, other than the detection probe, under the HPAassay conditions extant in the receptacle vessels 162 in thehybridization incubator 606. The label of this probe must bedistinguishable from the label of the detection probe.

After dispensing probe reagent into each of the receptacle vessels 162of the MTU 160, the pipette unit 480 moves to the pipette rinse basin1944, and the probe 481 of the pipette unit is rinsed with distilledwater.

The MTU carousel assembly 671 rotates the MTU 160 to the skewed disklinear mixer 634 where the MTU 160 and its contents are mixed, asdescribed above, at about 14 Hz to facilitate exposure of the targetamplicon to the added detection probes. The MTU 160 is then incubatedfor a period of time sufficient to permit hybridization of the detectionprobes to the target amplicon.

After hybridization incubation, the MTU 160 is again rotated withinincubator 606 by the MTU carousel assembly 671 to the pipetting positionbelow the pipette openings 662. A selection reagent stored in acontainer in the reagent cooling bay 900 is pipetted into eachreceptacle vessel 162 by the pipette unit 480. A selection reagent isused with the HPA assay and includes an alkaline reagent thatspecifically hydrolyzes acridinium ester label which is associated withunhybridized probe, destroying or inhibiting its ability tochemiluminesce, while acridinium ester label associated with probehybridized to target amplicon (or amplicon of the internal standard) isnot hydrolyzed and can chemiluminesce in a detectable manner underappropriate detection conditions.

Following addition of the selection reagent to each of the receptaclevessels 162 of the MTU 160, the pipette probe 481 of the pipette unit480 is rinsed with distilled water at the pipette rinse basin 1944. TheMTU 160 is rotated by the MTU carousel assembly 671 within the incubator606 to the skewed disk linear mixer 634 and mixed, as described above,at about 13 Hz to facilitate exposure of the target amplicon to theadded selection reagent. The MTU is then incubated in the incubator 606for a period of time sufficient to complete the selection process.

After selection incubation is complete, the left-side transportmechanism 502 transfers the MTU 160 into an available ramp-down station700 that is accessible to the left-side transport mechanism 502 to coolthe MTU 160. After the MTU 160 is cooled, it is retrieved from theramp-down station by the left-side transport mechanism 502 and is movedby the transport mechanism 502 into the active temperature and pre-readcool-down incubator 602 to stabilize the temperature of the MTU 160 atabout 40° C.

When a period sufficient to stabilize the temperature of the MTU 160 haspassed, the MTU carousel assembly 671 within active temperature andpre-read cool-down incubator 602 rotates to present the MTU 160 at theright-side distributor door of the incubator 602. The right-sidedistributor door 622 is opened and the MTU 160 is removed from activetemperature and pre-read cool-down incubator 602 by right-side transportmechanism 500.

The right-side transport mechanism 500 moves the MTU to a bar codescanner (not shown) which scans MTU bar code information posted on thelabel-receiving surface 175 of the label-receiving structure 174 of theMTU 160. The bar code scanner is preferably attached to an outer wall ofthe housing of the luminometer 950. A preferred bar code scanner isavailable from Opticon, Inc., of Orangeburg, N.Y., as part numberLHA1127RR1S-032. The scanner verifies the total time of assay prior toentering the luminometer 950 by confirming the correct MTU at thecorrect assay time. From the bar code reader, the right-side transportmechanism 500 moves the MTU 160 to the luminometer 950.

In a preferred mode of operation, before the right-side transportmechanism 500 moves the MTU 160 into the luminometer 950, the MTU 160 isplaced by the right-side transport mechanism 500 into an available MTUramp-down station, or chiller, to decrease the temperature of the MTU160 to 24±3° C. It has been determined that the MTU contents exhibit amore consistent chemiluminescent “light-off” at this cooler temperature.

Luminometer

Referring to FIGS. 40-42C, a first embodiment of the luminometer 950includes an electronics unit (not shown) within a housing 954. Aphotomultiplier tube (PMT) 956 linked to the electronics unit extendsfrom within the housing 954 through a PMT plate 955, with the front endof the PMT 956 aligned with an aperture 953. A preferred PMT isavailable from Hamamatsu Corp. of Bridgewater, N.J. as model number HC135. Signal measurements using the preferred PMT are based on the wellknown photon counter system.

The aperture 953 is centered in an aperture box 958 in front of the PMTplate 955. The aperture 953 and aperture box 958 are entirely enclosedby a housing, defined by a floor plate 964, a top plate 966, the PMTplate 955, and a back frame 965 and back plate 967, which prevents straylight from entering the aperture 953 and which is attached to the datumplate 82. An MTU transport path extends through the housing in front ofthe aperture 953, generally transversely to an optical axis of theaperture. MTUs 160 pass through the luminometer 950 via the MTUtransport path. A back rail 991 and a front rail 995 are disposed onopposite sides of the MTU transport path and provide parallel horizontalflanges which support the connecting rib structure 164 of an MTU 160disposed within the luminometer 950. Revolving doors 960 are supportedfor rotation within associated door housings 961 disposed on oppositeends of the MTU transport path and are turned by door motors 962, whichmay comprise stepper motors or DC gear motors.

The door housings 961 provide openings through which MTUs 160 can enterand exit the luminometer 950. An MTU 160 enters the luminometer 950 bymeans of the right-side transport mechanism 500 inserting the MTU 160through one of the door housings 961. The MTU 160 exits the luminometerunder the influence of an MTU transport assembly, various embodiments ofwhich are described below, which moves MTUs through the MTU transportpath and eventually out of the luminometer through the other doorhousing 961.

Revolving doors 960 are generally cylindrical and include a cut-outportion 963. Each revolving door 960 can be rotated between an openposition, in which the cut-out portion 963 is generally aligned with theopening of the associated door housing 961, so that an MTU 160 can passthrough the opening, and a closed position, in which a side of therevolving door opposite the cut-out portion 963 extends across theopening of the associated door housing 961 so that neither an MTU 160nor light can pass through the opening. Except when an MTU 160 isentering or exiting the luminometer 950, the revolving doors 960 arepreferably in their respective closed positions to prevent stray lightfrom entering the luminometer. Because test results are ascertained bythe amount of light detected by the PMT 956, stray light from sourcesother than the receptacle 160 being sampled can cause erroneous results.

As shown in FIGS. 40-42C, the MTU transport assembly may include an MTUadvance motor 972 which drives a lead screw 974 through a timing belt(not shown) or bevel gears (not shown). A screw follower 976 engaged tothe lead screw 974 is coupled to an MTU bracket 977 extending away fromlead screw 974 to engage the MTU 160. The MTU bracket 977 has a guideflange 978 with an elongated, slightly arcuate guide hole 979 formedtherein. A guide rod 980 extends through the luminometer 950 adjacentand parallel to the lead screw 974. Guide rod 980 extends through guidehole 979.

To advance the MTU bracket 977 (from bottom to top in FIG. 42C), thelead screw 974 turns counter-clockwise, as viewed in FIG. 42B. Due tosystem friction, the screw follower 976 and the MTU bracket 977 willalso turn counter-clockwise with the lead screw 974 until the guide rod980 contacts the left-side of the guide hole 979. When guide rod 980contacts the side of guide hole 979, MTU bracket 977 and screw follower976 can no longer rotate with lead screw 974, and further rotation ofthe lead screw 974 will cause the MTU bracket 977 and screw follower 976to advance along the lead screw 974. Arms 981 extending from the MTUbracket 977 will also rotate counter-clockwise over a limited arc toengage the MTU 160 and advance it through the luminometer 950, as thelead screw 974 rotates.

After the MTU 160 has passed the PMT 956, that MTU is ejected from theluminometer 950 and the next MTU can be pulled through the luminometer950. The MTU bracket 977 moves toward the MTU entrance end of the MTUtransport path by clockwise rotation of the lead screw 974. Systemfriction will cause the screw follower 976 and MTU bracket 977 to rotateclockwise until the guide rod 980 contacts the right-side of guideopening 979, after which, continued rotation of the lead screw 974 willcause the screw follower 976 and the MTU bracket 977 to retreat alongthe lead screw 974. This clockwise movement of the MTU bracket 977 willcause the arms 981 to rotate clockwise over a limited arc to disengagefrom the MTU, so the MTU bracket 977 can retreat without contacting theMTU. That is, the arms 981 will pass over the top of the MTU as the MTUbracket 977 retreats

As shown in FIG. 41, a blinder 982, driven by a blinder actuator 993,moves vertically up and down, in alignment with the aperture 953.Blinder 982 includes a front panel 983 which is mounted for slidingmovement with respect to the aperture box 958 and which includes agenerally rectangular opening (not shown) formed therein which can bealigned with the aperture 953. A top portion of the front panel 983blocks the aperture 953 when the opening formed in panel 983 is notaligned with the aperture 953 and thus operates as a shutter for theaperture 953. The blinder 982 includes two side-walls 987, arranged inparallel on opposite sides of the opening and generally perpendicular tothe front panel 983, and a back wall 988 spanning the back edges of thesidewalls 987 opposite the front wall 983 and generally parallel to thefront wall 983. The side-walls 987 and the back wall 988 define apartial rectangular enclosure sized to accommodate one receptacle vessel162 of the MTU 160 when the blinder 982 is moved up beneath one of thereceptacle vessels 162 of an MTU 160 by the blinder actuator 993.Blinder actuator 993 may be a linear stepper actuator including astepper motor 992 and a lead screw 994. HSI linear stepper actuators,available from Haydon Switch and Instrument, Inc. of Waterbury, Conn.have been used.

After the MTU 160 is placed into the luminometer 950 by the right-sidetransport mechanism 500, the motor 972 is energized to pull the firstreceptacle vessel of the MTU into alignment with the aperture 953. Theblinder 982, which is normally stowed out of the MTU transport path, israised by the blinder actuator 993 until the side walls 987 and backwall 988 of the blinder 982 surround the receptacle vessel 162 and theopening formed in the front panel 983 of the blinder 982 is aligned withthe aperture 953. The blinder 982 substantially prevents light fromsources other than the receptacle vessel 162 in front of the aperture953 from reaching the aperture 953, so that the PMT 956 detects onlylight emissions from the receptacle vessel directly in front of theaperture 953.

With the PMT shutter open, different detecting reagents (Detect I andDetect II), drawn from containers 1146, 1170 of the lower chassis 1100,are sequentially delivered into the aligned receptacle vessel 162through dedicated delivery lines (not shown) extending to a reagent port984 at the top of the luminometer 950. The Detect I and Detect IIreagents are hydrogen peroxide-containing and sodiumhydroxide-containing reagents, respectively, and combine to form a basichydrogen peroxide solution which enhances the chemiluminescence ofacridinium ester label which has not been hydrolyzed. Because basichydrogen peroxide is unstable, the Detect I and Detect II reagents arepreferably combined in the receptacle tube 162 just prior to detectionin the luminometer 950.

After the addition of Detect II, the light emitted from the contents ofthe receptacle vessel 162 is detected using the PMT 956 and the PMTshutter is then closed. The PMT 956 converts light emitted bychemiluminescent labels into electrical signals processed by theelectronics unit and thereafter sent to the controller 1000 or otherperipheral unit via cables (not shown) linked to a connector 986.

In cases where less sensitivity is required, it may be possible to usean optical sensor in place of a photomultiplier tube. A diode is anexample of an acceptable optical sensor which can be used with theluminometer 950. An optical sensor may also be appropriate when thematerial of the MTU 160 is relatively transparent, rather than thetranslucent appearance of the preferred polypropylene material. Whenselecting a material for the MTU 160, care should be taken to avoidmaterials that naturally luminesce or are predisposed to electrostaticbuild-up, either of which can increase the chances of a false positiveor interfering with quantification measurements.

The above-described process is repeated for each receptacle vessel 162of the MTU 160. After the chemiluminescent signal from each receptaclevessel 162 of the MTU 160 has been measured, the motor 972 advances tomove the MTU 160 through the exit door 961 and out of the luminometer950 and into the amplicon deactivation station 750.

An alternate, and presently preferred, luminometer is generallydesignated by reference number 1360 in FIG. 43. Luminometer 1360includes a housing 1372 having a bottom wall 1370, door assemblies 1200on opposite sides of the bottom wall 1370 which define end portions ofthe housing 1372, an optical sensor shutter assembly 1250 which definesa front wall of the housing 1370, a top wall (not shown), and a backwall (not shown), which complete the housing 1370 and define anenclosure therein. The right-side door assembly 1200 defines areceptacle entrance opening 1374, and the left-side door assembly 1200defines a receptacle exit opening 1376 through which a MTU 160 can bepassed into and out of the housing 1370. Each door assembly 1200controls access through the respective opening 1374 or 1376 andcomprises an end wall 1202, a cover plate 1232, and a rotating door 1220rotatably disposed between the end wall 1202 and the cover plate 1232.The optical sensor aperture shutter assembly 1250 controls lightentering an optical sensor (not shown in FIG. 43), for example aphotomultiplier tube. Luminometer 1360 includes a light receivermounting wall 1250 and a cover plate 1290 having an aperture 1292 formedtherein.

A bar code scanner 1368 is attached to a front portion of the housing1372 for scanning MTUs prior to their entry to the luminometer 1360.

A receptacle transport assembly 1332 moves a receptacle (e.g., a MTU160) through the luminometer 1360 from the entrance opening 1374 to theexit opening 1376. The assembly 1332 includes a transport 1342 movablycarried on a threaded lead screw 1340 that is rotated by a motor 1336coupled to the lead screw 1340 by a belt (not shown).

A dispensing nozzle 1362 is attached in the top wall (not shown) and isconnected by conduit tubes 1364 and 1366 to a pump and ultimately tobottles 1146 and 1170 in the lower chassis 1100. Nozzle 1362 dispensesthe “Detect I” and the “Detect II” reagents into the receptacles 162 ofthe MTU 160 within the housing 1372.

A receptacle vessel positioner assembly 1300 is disposed within thehousing 1372 and is constructed and arranged to position each tube 162of the MTU 160 in front of the aperture 1292 and to optically isolateeach tube being positioned from adjacent tubes, so that only light fromone tube at a time enters the aperture 1292. The positioner assembly1300 comprises a receptacle positioner 1304 rotatably mounted within apositioner frame 1302 that is secured to the floor 1370 of the housing1372.

The door assembly 1200 for the MTU entrance opening 1374 and exitopening 1376 of the luminometer 1360 is shown in FIG. 44. Door assembly1200 includes a luminometer end-wall 1202 which forms an end wall of theluminometer housing 1372. End-wall 1202 includes a first recessed area1206 with a second, circular recessed area 1208 superimposed on thefirst recessed area 1206. A circular groove 1207 extends about theperiphery of the circular recessed area 1208. A slot 1204, having ashape generally conforming to a longitudinal profile of an MTU 160, isformed in the circular recessed area 1208 to one side of the centerthereof. A short center post 1209 extends from the center of thecircular recessed area 1208.

The rotating door 1220 is circular in shape and includes an axial wall1222 extending about the periphery of the rotating door 1220. The axialwall 1222 is disposed a short radial distance from the outer peripheraledge of the rotating door 1220, thus defining an annular shoulder 1230about the outermost peripheral edge outside the axial wall 1222. A slot1226, having a shape generally conforming to the longitudinal profile ofan MTU is formed in the rotating door 1220 at an off-center position.

The rotating door 1220 is installed into the circular recessed area 1208of the end-wall 1202. A central aperture 1224 receives the center post1209 of the end-wall 1202, and circular groove 1207 receives axial wall1222. The annular shoulder 1230 rests on the flat surface of therecessed area 1206 surrounding the circular recessed area 1208.

End-wall 1202 includes a drive gear recess 1210 which receives therein adrive gear 1212 attached to the drive shaft of a motor 1213 (See FIG. 43in which only the motor 1213 for the right side door assembly 1200 isshown). Motor 1213 is preferably a DC gear motor. A preferred DC gearmotor is available from Micro Mo Electronics, Inc. of Clearwater, Fla.,under model number 1524TO24SR 16/7 66:1. The outer circumference of theaxial wall 1222 of the rotating door 1220 has gear teeth formed thereonwhich mesh with the drive gear 1212 when the shutter is installed intothe circular recess 1208.

The cover plate 1232 is generally rectangular in shape and includes araised area 1234 having a size and shape generally conforming to therecessed area 1206 of the end-wall 1202. Cover plate 1232 has formedtherein an opening 1236 having a shape generally conforming to thelongitudinal profile of an MTU, and, when the cover plate 1232 isinstalled onto the end-wall 1202, the raised rectangular area 1234 isreceived within the rectangular recessed area 1206 and opening 1236 isin general alignment with opening 1204. Thus, the rotating door 1220 issandwiched between the cover plate 1232 and the end-wall 1202, and theopenings 1236 and 1204 together define the entrance opening 1374 andexit opening 1376.

When the drive gear 1212 is rotated by the motor 1213, the rotating door1220, enmeshed with the drive gear 1212, is caused to rotate about thecenter post 1209. When the opening 1226 is aligned with openings 1204and 1236, MTUs 160 can be passed through the opening 1374 (1376) of thedoor assembly 1200. With the rotating door 1220 disposed within thecircular recessed area 1208 and the raised area 1234 of the cover plate1232 disposed within the recessed area 1206 of the end-wall 1202, asubstantially light-tight structure is achieved, whereby little or nolight enters through the door, when the opening 1226 is not aligned withopenings 1204 and 1236.

Optical slotted sensors are disposed within slots 1214 and 1216 disposedon the outer edge of the circular recessed area 1208 at diametricallyopposed positions. Preferred sensors are available from OptekTechnology, Inc. of Carrollton, Tex., model number OPB857. The slottedsensors disposed within slots 1214 and 1216 detect the presence of anotch 1228 formed in the axial wall 1222 to signal door open and doorclosed status.

The optical sensor aperture shutter assembly 1250 is shown in FIG. 45. Alight receiver, such as a photomultiplier tube 956, is coupled with alight receiver opening 1254 formed in a light receiver mounting wall1252. The light receiver mounting wall 1252 includes a generallyrectangular, two-tiered raised area 1256, which defines a generallyrectangular shoulder 1257 and a circular recessed area 1258 superimposedon the rectangular raised area 1256. A circular groove 1261 extendsabout the periphery of circular recessed area 1258. A center post 1259is positioned at the center of the circular recessed area 1258. Lightreceiver opening 1254 is formed in the circular recessed area 1258. Inthe illustrated embodiment, the light receiver opening 1254 is disposedbelow the center post 1259, but the light receiver opening 1254 could beplaced at any position within the circular recessed area 1258.

The aperture shutter assembly 1250 includes a rotating shutter 1270having an axial wall 1274 with gear teeth formed on the outer peripherythereof. Axial wall 1274 is formed near, but not at, the outer peripheryof the shutter 1270, thereby defining annular shoulder 1276. Rotatingshutter 1270 is installed in the circular recessed area 1258 with centerpost 1259 received within a central aperture 1272 formed in the rotatingshutter 1270 and with axial wall 1274 received within circular groove1261. A drive gear 1262 disposed within a gear recess 1260 and coupledto a drive motor 1263 meshes with the outer gear teeth formed on theaxial wall 1274 of the rotating shutter 1270 to rotate the rotatingshutter 1270 about the center post 1259. A preferred drive motor 1263 isa DC gear motor available from Micro Mo Electronics, Inc. of Clearwater,Fla., as model number 1524TO24SR 16/7 66:1. Micro Mo gear motors arepreferred because they provide a high quality, low backlash motor. Anopening 1280 is formed in the rotating shutter 1270 which can be movedinto and out of alignment with light receiver opening 1254 as therotating shutter 1270 is rotated.

With the shutter 1270 installed in the circular recessed area 1258, acover plate, or sensor aperture wall, 1290 is installed onto the sensormount 1252. As shown in FIG. 45A, sensor aperture wall 1290 includes agenerally rectangular, two-tiered recessed area 1296 which defines agenerally rectangular shoulder 1297 and which is sized and shaped toreceive therein the rectangular raised area 1256 of the sensor mount1252. A sensor aperture 1292 is formed through the aperture wall 1290and is generally aligned with the light receiver opening 1254 formed inthe sensor mount 1252. The sensor aperture 1292 is generally in theshape of an elongated oval having a width generally corresponding to thewidth of an individual receptacle vessel 162 of an MTU 160 and a heightcorresponding to the height of the intended viewing area. Althoughopening 1280 of shutter 1270 is shown in the illustrated embodiment tobe circular, opening 1280 can have other shapes, such as rectangular,with a width corresponding to the width of a receptacle vessel 162 or anelongated oval similar to sensor aperture 1292. Rotation of the rotatingshutter 1270 to a position in which the opening 1280 is aligned with thelight receiver opening 1254 and the sensor aperture 1292 permits lightto reach the PMT 956, and rotation of the rotating shutter 1270 to aposition in which the opening 1280 is not aligned with light receiveropening 1254 and sensor aperture 1292 prevents light from reaching thePMT 956.

Slotted optical sensors are disposed in slots 1264 and 1266 and detect anotch 1278 formed in the axial wall 1274 of the shutter 1270 to detectopened and closed positions of the shutter 1270. Preferred slottedoptical sensors are available from Optek Technology, Inc., ofCarrollton, Tex., as model number OPB857.

The aperture wall 1290 includes an upwardly facing shoulder 1294extending across the width thereof. A downwardly facing shoulder of theMTU 160, defined by the connecting rib structure 164 of the MTU 160 (seeFIG. 58), is supported by the shoulder 1294 as the MTU 160 slidesthrough the luminometer.

The receptacle vessel positioner assembly 1300 is shown in FIGS. 46 and48-49. The receptacle vessel positioner 1304 is operatively disposedwithin the receptacle vessel positioner frame 1302. The receptaclevessel positioner 1304 is mounted in the receptacle vessel positionerframe 1302 for rotation about a shaft 1308. Shaft 1308 is operativelycoupled to a rotary solenoid, or, more preferably, a gear motor 1306, toselectively rotate the receptacle vessel positioner 1304 between theretracted position shown in FIG. 46 and the fully extended positionshown in FIG. 48. A preferred gear motor drive is available from MicroMo Electronics, Inc. of Clearwater, Fla., as model number 1724TO24S+16/7134:1+X0520.

As shown in FIG. 47, the receptacle vessel positioner 1304 includes aV-block structure 1310 defining two parallel walls 1312. Receptaclevessel positioner 1304 further includes an area at the lower end thereofwhere a portion of the thickness of the receptacle vessel positioner1304 is removed, thus defining a relatively thin arcuate flange 1314.

When an MTU 160 is inserted into the luminometer 1360, the receptaclevessel positioner 1304 is in the retracted position shown in FIG. 46.When an individual receptacle vessel 162 is disposed in front of thesensor aperture 1292 (see FIG. 45A), so that a sensor reading of thechemiluminescence of the contents of the receptacle vessel 162 can betaken, the receptacle vessel positioner 1304 rotates forwardly to theengaged position shown in FIG. 49. In the engaged position shown in FIG.49, the V-block 1310 engages the receptacle vessel 162, thus holding thereceptacle vessel in the proper position in alignment with the lightreceiver aperture 1292 of the luminometer. As shown in FIG. 45, aperturewall 1290 includes a protrusion 1298 extending from the back of wall1290 into the MTU passage of the luminometer. The protrusion 1298 isaligned with the aperture 1292 so that when the receptacle vesselpositioner 1304 engages a receptacle vessel 162, the receptacle vesselis pushed laterally and encounters protrusion 1298 as a hard stop, thuspreventing the receptacle vessel positioner 1304 from significantlytilting the receptacle vessel 162 within the MTU passage. The parallelsidewalls 1312 of the V-block 1310 prevent stray light from adjacentreceptacle vessels 162 of the MTU 160 from reaching the light receiverwhile a reading is being taken of the receptacle vessel 162 disposeddirectly in front of the aperture 1292.

A slotted optical sensor 1318 is mounted to a lower portion of the frame1302, with the arcuate flange 1314 operatively positioned with respectto the sensor 1318. A preferred slotted optical sensor is available fromOptek Technology, Inc., of Carrollton, Tex., as model number OPB930W51.An opening 1316 is formed in the flange 1314. Opening 1316 is properlyaligned with the sensor 1318 when the receptacle vessel positioner 1304engages a receptacle vessel 162 and the receptacle vessel 162 andprotrusion 1298 prevent further rotation of the receptacle vesselpositioner 1304. If a receptacle vessel 162 is not properly positionedin front of the receptacle vessel positioner 1304, the receptacle vesselpositioner 1304 will rotate forwardly to the position shown at FIG. 48,in which case opening 1316 will not be aligned with the sensor 1318 andan error signal will be generated.

If a gear motor 1306 is employed for rotating the receptacle vesselpositioner 1304, it is necessary to provide a second sensor (not shown)to generate a positioner-retracted, i.e., “home”, signal to shut off thegear motor when the receptacle vessel positioner 1304 is fullyretracted, as shown in FIG. 46. A preferred sensor is available fromOptek Technology, Inc. of Carrollton, Tex. as model number OPB900W.

The MTU transport assembly 1332 is shown in FIG. 50. The MTU transportassembly 1332 is operatively positioned adjacent a top edge of anintermediate wall 1330 (not shown in FIG. 43) of the luminometer 1360.Intermediate wall 1330, which defines one side of the MTU transport paththrough the luminometer housing 1372, includes a rectangular opening1334. The receptacle vessel positioner frame 1302 (see, e.g., FIG. 48)is mounted to the intermediate wall 1330 proximate the opening 1334, andthe receptacle vessel positioner 1304 rotates into engagement with anMTU 160 through the opening 1334.

The MTU transport 1342 is carried on the threaded lead screw 1340 andincludes a screw follower 1344 having threads which mesh with thethreads of the lead screw 1340 and an MTU yoke 1346 formed integrallywith the screw follower 1344. As shown in FIG. 51, the MTU yoke 1346includes a longitudinally-extending portion 1356 and twolaterally-extending arms 1348 and 1350, with a longitudinal extension1352 extending from the arm 1350. The lead screw 1340 is driven, via adrive belt 1338, by the stepper motor 1336. A preferred stepper motor isa VEXTA motor, available from Oriental Motors Ltd. of Tokyo, Japan,model PK266-01A, and a preferred drive belt is available from SDP/SI ofNew Hyde Park, N.Y.

When an MTU 160 is inserted into the MTU transport path of theluminometer 950 by the right-side transport mechanism 500, the firstreceptacle vessel 162 of the MTU 160 is preferably disposed directly infront of the sensor aperture 1292 and is thus properly positioned forthe first reading. The width of the yoke 1346 between the lateral arms1348 and 1350 corresponds to the length of a single MTU 160. Thetransport 1342 is moved between a first position shown in phantom inFIG. 50 and a second position by rotation of the lead screw 1340.Slotted optical sensors 1341 and 1343 respectively indicate that thetransport 1342 is in the either the first or second position. Due tofriction between the lead screw 1340 and the screw follower 1344, theMTU transport 1342 will have a tendency to rotate with the lead screw1340. Rotation of the MTU transport 1342 with the lead screw 1340 ispreferably limited, however, to 12 degrees by engagement of a lowerportion of the yoke 1346 with the top of the intermediate wall 1330 andengagement of an upper stop 1354 with the top cover (not shown) of theluminometer housing 1372.

To engage the MTU that has been inserted into the luminometer 1360, thelead screw 1340 rotates in a first direction, and friction within thethreads of the screw follower 1344 and the lead screw 1340 causes thetransport 1342 to rotate with lead screw 1340 upwardly until the upperstop 1354 encounters the top cover (not shown) of the luminometer 1360.At that point, continued rotation of the lead screw 1340 causes thetransport 1342 to move backward to the position shown in phantom in FIG.50. The lateral arms 1348, 1350 pass over the top of the MTU as thetransport 1342 moves backward. Reverse rotation of the lead screw 1340first causes the transport 1342 to rotate downwardly with the lead screw1340 until a bottom portion of the yoke 1346 encounters the top edge ofthe wall 1330, at which point the lateral arms 1348 and 1350 of the yoke1346 straddle the MTU 160 disposed within the luminometer 1360.

The MTU transport mechanism 1332 is then used to incrementally move theMTU 160 forward to position each of the individual receptacle vessels162 of the MTU 160 in front of the optical sensor aperture 1292. Afterthe last receptacle vessel 162 has been measured by the light receiverwithin the luminometer, the transport 1342 moves the MTU 160 to aposition adjacent the exit door, at which point the lead screw 1340reverses direction, thus retracting the transport 1342 back, asdescribed above, to an initial position, now behind the MTU 160.Rotation of the lead screw 1340 is again reversed and the transport 1342is then advanced, as described above. The exit door assembly 1200 isopened and the longitudinal extension 1352 of the yoke 1346 engages theMTU manipulating structure 166 of the MTU 160 to push the MTU 160 out ofthe luminometer exit door and into the deactivation queue 750.

Deactivation Station

In the amplicon deactivation station 750, dedicated delivery lines (notshown) add a deactivating solution, such as buffered bleach, into thereceptacle vessels 162 of the MTU 160 to deactivate the remaining fluidin the MTU 160. The fluid contents of the receptacle vessels areaspirated by tubular elements (not shown) connected to dedicatedaspiration lines and collected in a dedicated liquid waste container inthe lower chassis 1100. The tubular elements preferably have a length of4.7 inches and an inside diameter of 0.041 inches.

An MTU shuttle (not shown) moves the MTUs 160 incrementally (to theright in FIG. 3) with the delivery of each subsequent MTU 160 into thedeactivation station 750 from the luminometer 950. Before an MTU can bedelivered to the deactivation queue 750 by the luminometer 950, the MTUshuttle must be retracted to a home position, as sensed by astrategically positioned optical slot switch. After receiving an MTU 160from the luminometer, the shuttle moves the MTU 160 to a deactivationstation where the dedicated delivery lines connected to dedicatedinjectors dispense the deactivating solution into each receptacle vessel162 of the MTU 160. Previous MTUs in the deactivation queue, if any,will be pushed forward by the distance moved by the MTU shuttle. Sensorsat the deactivation station verify the presence of both the MTU and theMTU shuttle, thus preventing the occurrence of a deactivating fluidinjection into a non-existent MTU or double injection into the same MTU.

An aspiration station (not shown) includes five, mechanically coupledaspirator tubes mounted for vertical movement on an aspirator tube rackand coupled to an actuator for raising and lowering the aspirator tubes.The aspiration station is at the last position along the deactivationqueue before the MTUs are dropped through a hole in the datum plate 82and into the waste bin 1108. Each time an MTU moves into thedeactivation station, the aspirator tubes cycle up and down one time,whether an MTU is present in the aspiration station or not. If an MTU ispresent, the aspirator tubes aspirate the fluid contents from the MTU.When the next MTU is moved into the deactivation station by the MTUshuttle, the last-aspirated MTU is pushed off the end of thedeactivation queue and falls into the waste bin 1108.

The steps and sequence of the above-described assay procedure performedon the analyzer 50 in the preferred mode of operation are graphicallyand succinctly described in the document Gen-Probe TIGRIS Storyboardv.1.0, Jun. 23, 1997, a copy of which was filed with the provisionaldisclosure upon which priority is claimed for the present specificationand the contents of which are hereby incorporated by reference.

Ideally, the analyzer 50 can run about 500 preferred assays in an 8 hourperiod, or about 1,000 preferred assays in a 12 hour period. Once theanalyzer 50 is set-up and initialized, it ordinarily requires little orno operator assistance or intervention. Each sample is handledidentically for a given assay, although the analyzer is capable ofsimultaneously performing multiple assay types in which different MTUsmay or may not be handled identically. Consequently, manual pipetting,incubation timing, temperature control, and other limitations associatedwith manually performing multiple assays are avoided, thereby increasingreliability, efficiency, and throughput. And because an operator'sexposure to samples is generally limited to the loading of samples,risks of possible infection are greatly reduced.

While the invention has been described in connection with what arepresently considered to be the most practical and preferred embodiments,it is to be understood that the invention is not to be limited to thedisclosed embodiments, but, on the contrary, is intended to covervarious modifications and equivalent arrangements included within thespirit and scope of the appended claims.

Furthermore, those of the appended claims which do not include languagein the “means for performing a specified function” format permittedunder 35 U.S.C. §112(¶6), are not intended to be interpreted under 35U.S.C. §112(¶6) as being limited to the structure, material, or actsdescribed in the present specification and their equivalents.

1. A process for isolating and amplifying a target sequence contained ina target nucleic acid present in a fluid sample, the process comprisingthe steps of: separating the target nucleic acid from other materialpresent in the fluid sample in a separation station; transporting areaction receptacle containing the separated target nucleic acid fromthe separation station to an amplification incubation station comprisingone or more temperature-controlled incubators; and incubating thecontents of the reaction receptacle, to which one or more amplificationreagents have been provided, in the amplification incubation station fora period of time and under conditions sufficient to permit the targetsequence to be amplified, wherein the separation and amplificationincubation stations are contained within a housing, and wherein each ofthe separating, transporting and incubating steps is automated.
 2. Theprocess of claim 1 further comprising providing to the reactionreceptacle a probe for a period of time and under conditions sufficientto permit the probe to hybridize to the target sequence or an ampliconthereof.
 3. The process of claim 2, wherein the probe includes adetectable label.
 4. The process of claim 3, wherein the label is afluorescent dye or a chemiluminescent compound.
 5. The process of claim2 further comprising detecting the presence or absence of the probehybridized to the target sequence, or an amplicon thereof, as anindication of the presence or absence of members of a target group oforganisms or viruses in the fluid sample, wherein the target groupconsists of at least one organism or virus.
 6. The process of claim 5,wherein the detecting step comprises determining the amount of lightemitted from the reaction receptacle as an indication of the presence orabsence of members of the target group of organisms or viruses in thefluid sample.
 7. The process of claim 5 further comprising determiningthe amount of members of the target group of organisms or viruses in thefluid sample.
 8. The process of claim 5 further comprising transportingthe reaction receptacle from the amplification incubation station to ahybridization incubation station within the housing prior to providingthe probe to the reaction receptacle, wherein the hybridizationincubation station comprises one or more temperature-controlledincubators, and wherein the step of transporting the reaction receptaclefrom the amplification incubation station to the hybridizationincubation station is automated.
 9. The process of claim 8, wherein theprobe is provided to the reaction receptacle after transporting reactionreceptacle amplification incubation station to the hybridizationincubation station.
 10. The process of claim 8 further comprisingtransporting the reaction receptacle from the hybridization incubationstation to a detection station within the housing prior to the detectingstep, wherein the presence or amount of hybridized probe is determinedin the detection station, and wherein the step of transporting thereaction receptacle from the hybridization incubation station to thedetection station is automated.
 11. The process of claim 10, wherein thedetection station includes a luminometer for determining the amount oflight emitted by the contents of the reaction receptacle.
 12. Theprocess of claim 1 further comprising raising or lowering thetemperature of the contents of the reaction receptacle prior totransporting the reaction receptacle to the amplification incubationstation.
 13. The process of claim 8 further comprising raising orlowering the temperature of the contents of the reaction receptacleprior to transporting the reaction receptacle to at least one of theamplification and hybridization incubation station.
 14. The process ofclaim 10 further comprising providing to the reaction receptacle adeactivating reagent for destroying nucleic acids present in thereaction receptacle.
 15. The process of claim 14, wherein thedeactivating reagent comprises a chemical agent selected from the groupconsisting of solutions of potassium permanganate, formic acid,solutions of sodium hypochiorite, hydrazine, and dimethyl sulfate. 16.The process of claim 14 further comprising transporting the reactionreceptacle from the detection station to a deactivation station withinthe housing prior to providing the deactivating reagent to the reactionreceptacle, wherein the step of transporting the reaction receptaclefrom the detection station to the deactivation station is automated. 17.The process of claim 1 further comprising providing to the fluid samplea solid support for a period of time and under conditions sufficient topermit the target nucleic acid to be immobilized, directly orindirectly, on the solid support prior to the separating step.
 18. Theprocess of claim 17, wherein the solid support comprises a magneticallyresponsive particle having a polynucleotide bound thereto.
 19. Theprocess of claim 18, wherein the target nucleic acid is hybridized to acapture probe prior to immobilizing the target nucleic acid on the solidsupport.
 20. The process of claim 18, wherein the fluid sample issubjected to a magnetic field during the separating step.
 21. Theprocess of claim 20 further comprising providing to the reactionreceptacle a probe for a period of time and under conditions sufficientto permit the probe to hybridize to the target sequence or an ampliconthereof.
 22. The process of claim 21 further comprising detecting thepresence or absence of the probe hybridized to the target sequence, oran amplicon thereof, as an indication of the presence or absence ofmembers of a target group of organisms or viruses in the fluid sample,wherein the target group consists of at least one organism or virus. 23.The process of claim 22 further comprising transporting the reactionreceptacle from the amplification incubation station to a hybridizationincubation station within the housing prior to providing the probe tothe reaction receptacle, wherein the hybridization incubation stationcomprises one or more temperature-controlled incubators, and wherein thestep of transporting the reaction receptacle from the amplificationincubation station to the hybridization incubation station is automated.24. The process of claim 23, wherein the probe is provided to thereaction receptacle after transporting the reaction receptacle from theamplification incubation station to the hybridization incubationstation.
 25. The process of claim 23 further comprising transporting thereaction receptacle from the hybridization incubation station to adetection station within the housing prior to the detecting step,wherein the presence or amount of hybridized probe is determined in thedetection station, and wherein the step of transporting the reactionreceptacle from the hybridization incubation station to the detectionstation is automated.
 26. The process of claim 17 further comprisingproviding to the reaction receptacle a deactivating reagent fordestroying nucleic acids present in the reaction receptacle.
 27. Theprocess of claim 26 further comprising transporting the reactionreceptacle from the detection station to a deactivation station withinthe housing prior to providing the deactivating reagent to the reactionreceptacle, wherein the step of transporting the reaction receptaclefrom the detection station to the deactivation station is automated. 28.The process of claim 1, wherein the transporting step is performed witha receptacle transport mechanism.
 29. The process of claim 1, whereinthe reaction receptacle comprises a plurality of receptacle vesselsformed as an integral array, each receptacle vessel containing the sameor a different fluid sample for simultaneously separating and amplifyingthe same or different target sequences present in the fluid samples ofthe receptacle vessels.
 30. The process of claim 1, wherein the housingdefines a self-contained, stand alone analyzer unit.
 31. The process ofclaim 30, wherein said analyzer unit is movable.
 32. The process ofclaim 1, wherein the material includes non-target nucleic acid.